In this study the contribution of the low-frequency residuals to the sea-level variability has been examined. This is done using 106-year old sea-level record obtained at Hoek van Holland. Computing the mean sea-level per season each year and the corresponding standard deviation one finds an increase in both these features of the sea-level record. The rise of the mean sea-level implies the effect of climate change. Moreover, it is found that the standard deviation in the sea-level, thus the intensity of variation, is the highest during fall and winter. This implies that the sea-level variability has a seasonal dependency. Furthermore, one finds an increase in the standard deviation on the long term. However, since a big part of the mean sea-level is influenced by tidal events, the increase in standard deviation is possibly linked to climate change in meteorological factors as has been found is in the study carried out by Gerkema and Duran-Matute(2017). With the use of the computational algorithms such as the Fast Fourier Transformation and the Wavelet Transformation one can extract the low-frequency residuals from the sea-level record. Inspired by the study of Gerkema and Duran-Matute(2017) a correlation between the wind speed and the low-frequency residuals have been found. Using the Wavelet Transformation it is found that the low-frequency residuals obtain the most energy during fall and winter, this empowers the finding that these low-frequency residuals are seasonal dependent. Moreover, when studying the low-frequency residuals closely it is found that the frequencies below 0.60 1 day obtain the most energy during fall and winter, especially the frequencies near 0.10 1 day . With these findings one can say that the contribution of the low-frequency signals, thus the low-frequency residuals, is correlated to meteorological events, such as the wind. Moreover, it is found that the variation in the low-frequency residuals is much smaller during spring and summer compared to the case during winter and fall. This seems not to be the case for the sea-level variability due to the tidal constituents and the high-frequency waves. Therefore, one may conclude that these low-frequency residuals contribute to a great extent in the standard deviation of the sea-level.

Shallow bays in the Caribbean, like Baie Orientale and Baie de L'Embouchure in Saint Martin, are often sheltered by coral reefs and covered by seagrass meadows. They provide valuable services as tourism and coastal protection. The ecosystems are linked through biological, chemical and physical processes. But they are under pressure due to sea-level rise. The response of one of the ecosystems to climate change could impact the other ecosystem. In order to predict the impact of sea-level rise on the biogeomorphology in Baie Orientale and Baie de L'Embouchure, the hydrodynamic model Delft3D Flexible Mesh is applied. The effect of seagrass meadows and coral reefs on both flow and waves are captured with this model. In this way, the long term change in average hydrodynamic conditions due to sea-level rise is determined depending on the response of the ecosystems. A wave-driven circulation is found in both bays with flows of 0.5 m/s over the reefs and currents of 0.2 m/s inside the bays. The hydrodynamic conditions are mainly determined by the reef height. Depending on the response of coral reefs to climate change and the amount of sea-level rise, the wave height inside the bays and the wave-induced currents increase. Under the worst-case scenario, where coral reefs degrade and seagrass meadows die, flow velocities increase by more than 100% in Baie de L'Embouchure and by 200% in Baie Orientale under a sea-level rise of 0.87 m. The significant wave height rises to 300% in Baie Orientale and doubles in Baie de L'Embouchure. But this increase of hydrodynamic stresses is not expected to lead to devastating damage to coral reefs and seagrass meadows. Instead, the response of coral reefs will be determined by changing water temperatures and ocean acidification. A shift in seagrass occurrence due to the changed hydrodynamics is expected. The long term impact of sea-level rise on the biogeomorphology of Baie de L'Embouchure and Baie Orientale seems to be limited. The ability to mitigate the impact of sea-level rise is shown and the resilience of the ecosystems proved, which is very promising for other shallow Caribbean bays that are threatened by sea-level rise.

KEY POINTS (I) A biophysical model framework (BMF) for corals is developed in which four environmental factors are included: (1) light; (2) hydrodynamics; (3) temperature; and (4) acidity. (II) The full feedback loop between corals and their environment forms the core of this model framework, where the morphological development is new and closes the feedback loop. (III) The developed BMF predicts the coral response to environmental input via (mainly) process-based relations within the accuracy of climate projections. (IV)- The BMF supports both the deep reef refugia hypothesis and the turbid reef refugia hypothesis. (V) The BMF contributes to the development of protection and recovery programs and is not site-specific. (VI) The BMF is developed for long-term predictions - in the order of decades to centuries - but runs on daily averages and is therefore applicable for assessing the response of corals on shorter time-scales; such as months to years. SUMMARY The increasing pressure on Earth’s ecosystems due to climate change becomes more and more evident. These pressures are especially visible at coral reefs. Therefore, a good understanding of the biophysical mechanisms controlling these ecosystems is needed, so that accurate predictions of their survival can be made. Such an understanding is also needed to develop efficient recovery and protection programs vital to the maintenance of these ecosystems. Because the research on marine ecosystems is relatively young and the phenomenon of coral bleaching is yet to be fully understood, there is no comprehensive framework in which the complex interactions between corals and their environment are combined. In this study, a biophysical model is developed in which four environmental factors are included in a feedback loop with the coral’s biology: (1) light; (2) hydrodynamics; (3) temperature; and (4) acidity. Literature from multiple disciplines is combined to find the interdependencies between the corals and their environment. These relations include coral growth, coral bleaching, storm damage, and recruitment/recolonization of corals. For the connection with the hydrodynamics, a coupling is made between the biological model developed here and Delft3D-FM. The composed biophysical model is a big leap forward in understanding the world of coral reefs, as it is the first construction of a model framework including four environmental factors in which the hydrodynamics are included in the feedback loop. Furthermore, it creates the ability to assess recovery and protection programs based on the four aforementioned environmental factors; e.g. the susceptibility of coral bleaching can be reduced by increasing the attenuation of light through the water column. Because more environmental factors have a role to play in the coral dynamics, the framework is constructed such that these can be added relatively easily.

Four kilometers west of the Norwegian island Fedje, mercury, leaking from the U-864 wreck, has highly polluted a seabed area of approximately 40 000 m2. The bow section of the wreck is located on a stability critical slope of 15 degrees. In 2016, Van Oord used a flexible fall pipe system to install a counter fill to stabilize the wreck and simultaneously cap a portion of the contaminated area. In the future, the Norwegian government plans to cap the complete area to prevent further dispersion of mercury. This research aims to gain more knowledge about the spreading of sediments during such an operation occurring under realistic hydrodynamic conditions. A more complete understanding of the process will allow for better risk assessment of future capping operations. To this end, the unique data set gathered during the counter fill project has been analyzed. In order to predict extreme flow events, the bottom currents are decomposed. By decomposing the erratic velocity signal, tidal (25 %) and inter-tidal residual current (38 %) components are identified and understood. However, the driving force for the remaining intra-tidal part, which contains the highest current anomaly events, cannot be identified. Evidence is found for the occurrence of internal waves providing a possible explanation. Due to a lack of data, a quantitative prediction cannot be made. Consequently, the exact maximum currents at the site are unpredictable, but stayed below 0.4 m/s during the project. During the installation work, high turbidity clouds have been measured. The origin is investigated by analyzing the particle size distribution and the mercury concentration of sediment samples; said samples are drawn from the capping material, the installed capping layer and sediment traps placed around the wreck. The findings indicate that the clouds are caused by a loss of clean material and are not from the contaminated seabed. This is supported by modeling the dispersal of clean particles from the flexible fall pipe. The promising results regarding the use of a flexible fall pipe for capping layer installation are not only applicable for the U-864 area but also for other polluted offshore areas.

In times of rapid urbanization, engineering interventions in coastal systems have become more common. It is important to understand the interplay of these engineered solutions with their natural environment to minimize hazardous side effects to our ecology, economy and coastal safety. In a numerical study by Rijnsburger (2021), a flow recirculation with a diameter of 10 to 20 km - similar to an eddy - was identified in the North Sea. It remained unclear what causes the recirculation, but its location in the Rhine region of freshwater influence and near the artificial Maasvlakte headland, suggest that the recirculation could both be baroclinic or barotropic. This numerical model study is set out to understand what processes drive the recirculation. Identifying these processes is important to understand what is required to properly model the hydrodynamics along the Dutch coast, and accordingly, the spreading of sediment, pollutants and phytoplankton. A realistic 3D hydrodynamic model was used to assess the recirculation during a validated spring-neap cycle. Our analysis shows that the recirculation has a maximum diameter of roughly 15 km during neap tide and 5 km during spring tide. The recirculation occurs in the buoyant top layer of the water column and grows offshore from its onset north of the Maasmond around HW+3 until it is overtaken by ebb tidal velocities around HW+5. This study shows that the onshore advection of negative (clockwise) vorticity water results in most water flowing back to the river mouth into an expanding clockwise recirculation, the vorticity and strength of which are strongly influenced by buoyant river outflow. Our analysis shows that the headland is not a prerequisite for its onset. Nevertheless, two mechanisms are identified of how the headland influences the recirculation. First, during spring tide, the headland is found to ‘shelter’ the recirculation from strong ambient currents in the midfield which would otherwise hamper the recirculation. Secondly, the geometry of the river mouth influences the vorticity input in the North Sea associated with the buoyant river outflow. To further investigate what processes influenced by the river outflow could contribute to the recirculation, a scale analysis and particle tracking study were deployed. Although, the study is not yet conclusive on what drives the onshore advection of the spinning water that flows into the recirculation, several potential processes have been identified. For future studies that want to model the spreading of freshwater, pollutants or suspended sediment near the river mouth of the Rhine-Meuse system, this study underlines the importance of using a three-dimensional numerical model that accounts for density differences and the influence of the studied recirculation. The latter is especially important when the boundaries of the numerical domain are located close to the river mouth, due to which the influence of the recirculation is not resolved unless explicitly accounted for in the boundary conditions. This study therefore contributes to the improvement of future modelling studies of the Rhine ROFI and to our understanding of the processes that govern the hydrodynamics along the Dutch coast.

This thesis investigates the important physical processes related to underwater sound propagation due to offshore pile driving with the first commercial and numerical model called the Underwater Acoustic Simulator (UAS). To make adequately use of noise mitigation measures during offshore wind projects and to protect marine life the prediction of sound levels in water is important. The aim of this thesis is to assess if the UAS is suitable to give insight in the physics contributing to sound propagation and if the UAS is suitable to quantify sound levels in water for the application in future wind park projects. This is done by comparing the predicted sound levels with the UAS with the measured sound levels obtained during the construction of the Gemini wind park. The results obtained with the UAS identify the parameters related to the seabed properties as the most important for governing the attenuation of the noise levels as function of distance and frequency. In the UAS the seabed is modelled as a fluid. Especially frequencies < 800 Hz are sensitive to the choice of geo-acoustic parameters. These frequencies show a trend of underestimation of the sound levels compared to the acoustic data. An increase of the predicted sound levels is observed for increasing the coarseness of the sediment of the upper seabed layer and decreasing this layer thickness. The UAS parameters can be tuned to obtain sound levels that agree with the measured sound levels in the Gemini area. However, these parameter values do not represent the properties of a realistic seabed. Additionally, no evident choice of values exist to arrive at sound levels that agree with the acoustic data. It is concluded that the choice of values compensates for the exclusion of the shear effect in the fluid approximation of the seabed in the UAS. The exclusion of the shear effect in the representation of the seabed in the UAS is regarded as essential. Tsouvalas (2015) shows that the propagation of sound energy at low frequencies is governed by the shear of the soil. These lower frequencies propagate in the deeper parts of the seabed where shear effects play a role. Also, sound energy in the form of Scholte waves propagates at the water-seabed interface, thereby contributing to the sound levels in water. The reason the sound levels propagating at low frequencies is sought in two aspects. In a fluid seabed the geo-acoustic parameters are adjusted and account for the damping associated with shear, while the propagation of sound energy at these wave forms is not modelled. Another possible explanation is the trapping of the low frequency pressure waves in the seabed. Although the UAS is able to predict sound levels in the Gemini area that agree well with the measured sound levels, this is not due to the correct implementation of the physic regarding the seabed. As a consequence, the model is tweaked to arrive at the measured. The UAS is therefore not considered suitable for application in future wind park projects.

This thesis introduces a new algorithm for optimising shipping routes within a dredging project. Highly dynamic and time-dependent hydrodynamic features influence shipping routes. Due to the complex interactions between the horizontal tide, vertical tide, stratifying forces, wind-driven forces, and limited water-depth, shipping routes were previously only optimised for large scale routes (order of 1000 km). This study presents an algorithm that can optimise shipping routes that are influenced by these small scales (order of 10 km) hydrodynamic features. This algorithm uses graph theory to solve for the time-dependent fastest path between start and destination. Graph theory searches for the optimal path through a set of nodes that are connected with edges. This study uses the time-dependent shortest path algorithm which accounts for the FIFO-criteria (Waiting criteria) and can solve the non-convex nature of the problem The input of this algorithm is a hydrodynamic model. These models are Computational Fluid Dynamic (CFD) models that calculate currents and water levels in a specific domain. The domain is discretised into cells and nodes to calculate these hydrodynamic features. This study uses the nodes of this hydrodynamic model as the vertices of the graph. However, for some cases, the hydrodynamic model has too many nodes for the shortest path algorithm. This study presents a method for reducing the number of nodes without reducing the spatial resolution. The nodes are reduced based on a combination of the vorticity and the magnitude of the flow. This algorithm is implemented in a python software package named Hydrodynamic Algorithm for Logistic enhancement Module (HALEM). HALEM can determine the optimal shipping route for a given hydrodynamic model. Defining different cost functions results in different optimisation purposes. This thesis presents cost functions for the fastest route, shortest route, cheapest route and least polluting route. This software is then implemented in the OpenCLSim software so that this combination of software can optimise routes of entire projects. A case study simulates a beach-nourishment at Schouwen Westkop Noord to demonstrate the practical use of HALEM and OpenCLSim. For this project, 425,500 m3 sand should be dredged offshore and pumped onto the beach. Due to the narrow gullies and tidal changes in hydrodynamic features, the routes were hard to predict. The simulation with HALEM and OpenCLSim shows an increase in the production with 21 % compared to the simulation with just OpenCLSim.

The Weddell Polynya, a large hole in the Antarctic sea ice, reappeared in 2017. The polynya forms due to deep convection, which is caused by static instability of the water column. Observations and model studies show periodic heat accumulation in the subsurface layer prior to a polynya. This heat accumulation could be caused by internal ocean dynamics: the Southern Ocean Mode. Periodic subsurface heat and salt accumulation could be the major driver in causing periodic deep convection, which is in contrast with earlier studies. These studies focus on surface processes, and see the polynya as an irregular event. In this study a simple convective model is used to look into this contrast. Model simulations excluding and including periodic subsurface heat and salt fluxes have been performed. Multiple polynya events were only simulated in the model set up including subsurface fluxes. The dominant frequency for polynya events in these simulations equals the frequency of the subsurface heat and salt accumulation. This frequency is still visible in runs with white noise added to the freshwater flux, showing the importance and dominance of the subsurface forcing. In combination with earlier studies, this study suggests that periodic subsurface processes are most dominant and govern the initial formation and periodicity of the Weddell Polynya.

Globally, at each river mouth freshwater is discharged to coastal waters. At each river mouth a freshwater plume is formed. These fresh water plumes are also known as the regions of freshwater influence (or ROFI’s). Furthermore, the freshwater plume will affect local coastal water levels. In order to improve global flood forecasting, research on this topic has been conducted. Through a combination of numerical (DFlow-fm) and probabilistic (vine copula) models predictions can be made for the size- and hydraulic effect of these river plumes.

TheAmazon-Orinoco river plume is a buoyant freshwater lens of 1.2 × 106km2, which has been traced over 2000 km from the Amazon river mouthinto the Caribbean Sea and along the Lesser Antilles. The river plume iswarmer than the surrounding open-ocean waters, with temperaturedifferences up to 1.5 ∘C caused by a stratification-induced barrier layerinhibiting vertical mixing and coloured matter increasing solar energyabsorption. Due to its magnitude, the river plume affects thehydrodynamics and the oceanic conditions in the Western Tropical NorthAtlantic (WTNA) substantially, but its variations on interannual time scales andthe corresponding relation to local sea-surface temperature (SST) are notwell understood. The Caribbean Sea is a region of high ecological value as itis home to extensive coral reefs, which are especially sensitive topersistent high SST. Therefore, this study investigates the interannualvariability of the Amazon-Orinoco river plume and its relationship to SSTsin the Caribbean Sea and the WTNA. It is hypothesised that fresh anomaliesof the river plume salinity pattern are indicative of a more extensivetransportation of the heat contained in the river plume. As a result, itis expected that interannual variations of dominant river plume pathwaysaffect the magnitude and location of anomalous SSTs. To test thishypothesis, model reanalysis fields of oceanic conditions from 1993 to 2017are used to conduct statistical analyses. In this context, the river plumevariability is determined using specific regions of freshwater influenceestablished using Empirical Orthogonal Function (EOF) analysis ofanomalous sea-surface salinity (SSS). Cross-correlations analysis relatingthese EOF modes of with atmospheric processes show that the interannualvariability of the river plume is dominated by wind-inducedadvective transport and -mixing. Strong winds along the Brazilian shelfare related locally increased SSS, while a weak southward component makesfor extensive spreading of the low-salinity plume waters. Additionally, weshow that high river discharge affects SSS east of the Lesser Antillesafter a lag of three months. Through its modulation of these atmosphericprocesses, there is a strong indication that the El Niño-SouthernOscillation affects SSS variability in the main along-shelf northwestplume pathway, with low SSS 1–9 months after a La Niña event. DecreasedSSS are found in phases 2 and 3 of the Madden-Julian Oscillation, whileincreased SSS was observed in phases 6 and 7. However, the evidence forthis relation is weak and should be investigated in further research. The results show that, opposed to the hypothesis,a more extensive river plume is not associated with higher SSTs in theCaribbean Sea. However, strong correlations are found between river plumesurface area and SSTs at a lag of 1 year. Based upon results of previousstudies, we argue that the river plume has the ability to pre-heat themixed layer in the WTNA leading to extreme temperatures in the followingyear. It is wise to conduct a Lagrangian parcel back-tracking experimentto verify this mechanism.

Coastal bays in the Caribbean accommodate different marine ecosystems, including seagrass meadows and coral reefs, which provide important ecosystem services. However, these marine ecosystems are endangered. Seagrass ecosystems have a key role in coastal bays, but despite their alarming rates of loss, they receive little attention compared to other marine ecosystems. This study aims to provide a better understanding of the role of seagrass ecosystems in coastal bays by assessing their impact on the morphodynamic behavior. In order to achieve this, an existing hydrodynamic model has been extended to include morphodynamics. Two different bays have been investigated: Baie Orientale and Baie de l’Embouchure (St. Martin). These bays represent a partially exposed and fully sheltered bay, respectively. Both regular wave conditions, as well as extreme storm conditions, have been investigated to understand the consequences of seagrass loss on coastal erosion for different environmental climates. The coastal erosion has been found to be more prominent in the exposed region, whereas the more sheltered areas are more resilient. The erosion takes place in shallow waters but remains limited under regular swell conditions. The increased wave energy, during the extreme storm event, increases the erosion rates considerably. However, the regular swell conditions are normative in shaping the morphological development of these coastal bays when longer timescales are considered. The seagrass counters erosion most effectively in the foreshore and much less in deeper regions. Removal of seagrass in the foreshore (between 1-3m) halves the sediment stabilization. In contrast, the sediment stabilization increases if the meadows are able to spread especially towards the shore. In addition, the wave energy and waveform have a significant impact on the sediment stabilization. The stabilization typically decreases for higher and shorter (storm) waves, whereas it increases for smaller and longer (swell) waves. The long-distance interactions between seagrass meadows and coral reefs have led to their mutual coexistence, which is also found to be beneficial for the erosion control of the coastal bays. The dissipation of wave energy on top of the reefs fosters the sediment stabilization by seagrass. Moreover, the impact of the reefs on sediment stabilization also increases in the presence of seagrass meadows due to the additional drag exerted by the seagrass. The seagrass meadows are typically more effective under swell waves, whereas the reefs are more dominant in the dissipation of storm waves. Seagrass meadows and coral reefs form thus a synergy, in which the stabilization of sediments provided by the individual ecosystems is facilitated, reinforced, and complemented by the proximate presence of the other ecosystem. Finally, the role of seagrass on sediment stabilization has been explored under climate change. The coastal erosion increases for the considered sea-level rise scenarios. The impact of the seagrass on sediment stabilization decreases when the bays, seagrass and reef ecosystems are not able to keep up with sea-level rise. The synergy between seagrass and reefs emphasizes that the responses of both ecosystems are of importance for the future of tropical sheltered bays and should therefore not be managed in isolation.

Subsea Rock Installation vessels cover pipelines, which transport oil from oil and gas fields. This is done by means of a flexible fallpipe until depths of 1000 meters. Around the Shetland Islands, the workability of the vessels at two specific project locations is compromised by the conditions in the ocean. In this research, data from a 3D hydrodynamic model and logged information from the vessels has been analysed and combined to find an explanation for these problems. At the second location, for tidal flow to the east or east-northeast in the bottom and middle part of the water column, it is highly likely that the working activities have to be interrupted. Moreover, if the value of the turbulent vertical eddy viscosity exceeds 0.028 m²/s, the chance on non-working conditions increases with 70%. For the other project location, these kind of correlations have not been observed.

The Atlantic Meridional Overturning Circulation (AMOC) is a key component in the Earth System. Given its important role in the climate system, variability in the AMOC strength is expected to have great impact on the global climate. The current observational timeseries are not long enough to make climate projections for the end of the century or even longer. Therefore, coupled climate models play an important role in the making of end of century climate projections on the AMOC strength. A known issue with the current generation of global coupled climate models is that the grid resolution is generally too coarse to resolve smaller scale processes such as mesoscale eddies. Observations and modelling studies suggest that mesoscale eddies play an important role in the exchange of water between convection regions and downwelling regions. When such processes are absent or parametrized incorrectly, it can have an influence on the climate projections based on these model simulations. This study analysed the AMOC characteristics in two different simulations of the Community Earth System Model; a reference simulation (referred to as piControl) and a simulation in which the atmospheric CO2 concentrations have been increased to four times the initial concentration (referred to as 1pctCO2). First, the AMOC characteristics in the piControl simulation are analysed using both a Eulerian and a Lagrangian approach. The Eulerian analysis shows that deep mixed layers, an indicator for convection, are present in the subpolar North Atlantic. Compared to observations and higher-resolution ocean-only models are these located closer to the West-Greenland coast. Strong vertical velocities are found over the continental slopes, especially over the steep continental slopes around Greenland. Second, the Lagrangian analysis showed the consequences of the coarse grid in the model. Only a single pathway around the subpolar gyre was observed. This implies that particles will experience convection while crossing the interior of the Labrador Sea, but only will experience downwelling when their individual pathway comes close enough to the continental slopes around Greenland. Furthermore, there is only limited exchange of particles with the regions north and south of the subpolar gyre. In the export of deep waters to the subtropical gyre, does it seem that the particles are being blocked by the North Atlantic Current. Third, the changes in the AMOC characteristics in the 1pctCO2 simulation are compared to the piControl simulation. In the 1pctCO2 simulation have deep mixed layers disappeared from the subpolar North Atlantic and convection in this region has shut down. A new fresh(er) surface layer in the Labrador Sea has intensified the stratification and prohibits the formation of deepmixed layers. Instead of the deep mixed layers in the subpolar North Atlantic have new deep mixed layers emerged between 30N and 40N. In general are velocities reduced in magnitude in the 1pctCO2 simulation, but the stronger vertical velocities can still be found over the continental slopes. In conclusion, the results show that the CESM model can reproduce the two components of the AMOC reasonably well, but the connection in the formof mesoscale eddies is missing. This illustrates that a overturning streamfunction simplifies the complexity of the overturning process. The overturning streamfunction is a measure for the overturning strength, but it does not take into account how and if the convection process and the exchange between convection and downwelling are represented.

Due to climate change and human interventions, saltwater intrusion is becoming a topic of increasing concern worldwide. Salt water intrudes into the Rotterdam Waterway (RWW) by an exchange flow, where the denser sea water propagates landwards at the bottom. The main competing mechanism for this stratified exchange flow is vertical mixing, which can be realised by internal wave induced shear instabilities or wave breaking. The goal of this study is to investigate whether internal waves generated over undular bottom topography in the RWW can generate additional vertical mixing. The underlying assumption is that a decrease in stratification decreases salt intrusion.   The approach to answer the main research question is a combination of an analytical and a numerical analysis. The analytical study is based on frictionless linear theory. Internal wave behaviour is further analysed with FinLab, a finite element model which includes the non-hydrostatic processes and effects of density differences. FinLab is evaluated for the application of this study by means of a validation case.  In the analytical study, linear theory is applied to obtain a relation between the bed wave parameters and average internal wave energy density E for internal waves generated over sinusoidal bottom topography in a linearly stratified fluid. The derived expression describes that the bottom topography amplitude h0 and bed wave number kT both have a positive quadratic relation with the energy. Additionally, kTkinfluences the resonance conditions.  To validate FinLab for internal wave breaking and mixing an experiment in a wave tank, according to an example from literature, is simulated. The validation case reveals a shortcoming in the turbulent mixing parameterization. However, on scales relevant for the RWW the effect of this will not have the same significance. The validation case offers a suggestion for a subgrid closure of diffusion, where density effects are taken into account.  Numerical simulations of a 2D channel stretch with sinusoidal bottom topography, a linearly stratified fluid and a linearly varying background velocity, show generation of resonant trapped internal waves for the first two resonant modes. These occurrences correspond to the highest values of kinetic energy as function of vertical velocity averaged over the bed wave domain. The vertical buoyancy flux b is downward directed during occurrences of internal waves and becomes upward directed for increasing background flow. Vertical mixing is associated with an increase in average potential energy Ep, which is 17% higher for the base case (containing bed waves) than for a similar case without bed waves. This increase is larger when bottom shear stress increases. Richardson numbers below 0.25, associated with shear instabilities and mixing, are only observed near the bed, mainly when internal waves are present. The effect of variations in bottom topography wavelength LT and amplitude h0 on internal wave energy can be explained by the analytical formulation. The effect of bed wave parameter changes on b and relative increase in Ep can be related to the effect of the changed amount of bed friction rather than the difference in wave energy.   The first resonant mode is the most energetic, however, the average energy density found for these waves is only 0.4% to 6.7% of the potential energy anomaly (PEA); the energy required to fully mix a stratified water column. In the simulations the only mechanism that could transfer internal wave energy to turbulent kinetic energy are shear instabilities near the bed. Over the full simulation, the net vertical buoyancy transport is of negligible magnitude, where Ep shows significant increases between 6% and 99% compared to similar cases without bed waves and is enhanced during the presence of internal waves.  The main discussion point is that the quantification of vertical mixing requires improvement, particularly to determine the importance of mixing by internal wave-induced shear instabilities and by bed shear. Mixing by local shear instabilities (of which the relevant scales cannot be resolved with the current grid resolution) does not have an adequate parameterization, because density effects are not included in the turbulence closure. The bed friction parameter, which greatly influences the behaviour of the system, has to be validated. Furthermore, cases where internal waves might break in practice (e.g. at banks) were not considered. Finally, the observed internal wave energy is of small magnitude, however field measurements by Pietrzak(1991) shows that turbulence production by internal waves was significant.   

The Labrador Sea is one of the deep convection sites in the world's oceans and the water masses formed here are an important component of the Atlantic Meridional Overturning Circulation (AMOC). To study this linkage, one study in particular used an idealized model of the Labrador Sea where the density variations consists only of temperature variations. In this study, it is questioned whether the assumption of neglecting salinity is appropriate, by analysing the pathways of water mass and water mass transformation in the Labrador Sea. This is investigated by using that same idealized model (here called the reference run) and comparing this to a model where salinity variations are added whilst keeping density variations the same (Sconstant) to produce a similar circulation pattern. Furthermore, a model configuration is created which investigates if a seasonal cycle in salinity impacts the circulation pattern of the Labrador Sea (Sseasonal). The pathways of water masses in these model configurations are analyzed by Lagrangian particle tracking from A to B. It was found that with the same initial density variations the maximum surface eddy kinetic energy (EKE) increases by 41 % when salinity is incorporated in the model. An increase in EKE is often associated with more water mass leaving the boundary current (BC) due to an increase in instabilities. Surprisingly, the opposite was found: 7.02 and 8.22 Sv are transported through the BC for the reference run and Sconstant, respectively. Furthermore it was found that most of the water mass leaves and re-enters the BC near the maximum EKE for each model configuration. An increase was found in maximum overturning in density space from an Eulerian perspective: from 3.9 to 4.8 Sv for the reference run and Sconstant, respectively, where about 10 % so called density compensation occurred for Sconstant. No significant annual changes are found when adding a seasonal cycle to the model. For all model configurations a large discrepancy exists between Eulerian and Lagrangian calculations in downwelling. This discrepancy is due to Lagrangian particles that reside in the models at the end of their simulation duration Thus the overturning in the Labrador Sea is significantly influenced by particles that have a long residence time (longer than 4 years in these model simulations). Between 22 and 25 % of the Lagrangian volume transport does not reach the outflow of each model simulation. There are also properties that salinity did not influence: no significant changes were found between the model configurations for the overturning in depth space, the annual MLD and barotropic streamfunction. In conclusion adding salinity to the idealized model showed only minor changes in the pathways of water mass and water mass transformation: the order of magnitude of all analyzed properties stays the same. Density compensation however is neglected when no salinity variations are added in the model. This means that for a highly idealized model of the Labrador Sea, salinity variations can be neglected, when density variations due to salinity variations are represented by temperature variations.

Regular maintainance dredging is a large expense to the Port of Rotterdam, therefore the installation of sediment traps is considered. By increasing the bathymetry locally, an increase of local accumulation is expected and a decrease deeper in the harbour basin. This thesis describes the functioning of sediment traps in a stratified tidally energetic estuary, where sediment is supplied by the river and sea. A numerical 2DV representation is set up for the Botlek Harbour with the hydrostatic Delft3D software. A calculated salinity time-series by Operationeel Stromingsmodel Rotterdam (OSR) is combined with a measured water level time series for the same time period to describe the hydrodynamic boundary conditions. Simulations are done with a variable and constant Suspended Particulate Matter (SPM) time series boundary conditions, that were generated based on the measurements of De Nijs (2012). Flow expansion caused by the sediment trap reduces the flow velocity, but increases the turbulent kinetic energy locally. A reduction of bed shear stress is observed in the trap, except near the edges where an increase is observed. Density currents caused by salinity differences govern the vertical flow velocity distributions, while tidal filling causes the net exchange. The depth of the trap plays a significant role in the internal flow characteristics. The sediment trap changes the properties of the internal flow, which may change the hydraulic state of the flow, i.e. from supercritical to subcritical, resulting in large instabilities and even an internal hydraulic jump. Shallow sediment traps result in less frequent internal hydraulic jump and weaker jumps compared to deeper sediment traps. To investigate the dominant mechanism for the trapping of sediment in the sediment trap, a distinction is made between an erosion and a fluid mud scenario. The erosion scenario shows the largest agreement with the survey data, i.e. maintenance dredging data and Echosounder multibeam surveys, but contribute only marginally to the trapping of sediment. The fluid mud scenario yields the largest contribution to the trapping of sediment. The decreased amounts of accumulated sediment in the basin for substantial to lots of fluid mud behaviour may vary between 10% and 14%, depending on how this fluid mud behaviour is modelled. Various shapes have been tested on erosion and fluid mud scenarios. Both for erosion and fluid mud a more extreme choice of parameters might yield also more extreme results, this is however not considered realistic. The creation of an overdepth has shown to result in a marginal improvement in the capturing of sediment in an environment where erosion is important. A regular sediment trap decreases accumulation in the harbour basins by 2%. A trap twice as shallow increases this amount to 4%, but deepening the trap further may even enhance accumulation in the basins. A shorter or longer trap did not improve the situation. Installation of a sill did however result in a decrease of 6% compared to the situation without trap. It is concluded that this effect can be largely contributed to the internal flow properties and the presence of internal hydraulic jumps. The presence of an overdepth results in a significant improvement in the capturing of fluid mud flow. For the trapping of fluid mud flow, an overdepth results in 6% less sediment in the harbour basins no matter the depth or shape of the trap. The length of the trap did influence the accumulation in the basins. A trap twice as short shows an increase of 4 % of accumulation in the basins compared to a regular trap. A trap twice as long or installation of a sill results in similar accumulation in the harbour basins as a regular trap. For fluid mud flows, any type of overdepth decreases accumulation of sediment considerably. The amount of overdepth or the shape does not influence this. The length of the trap should be sufficient. A trap that is too short results in an increase of accumulation in the basins. For environments where erosion is important, only shallow sediment traps have proven to reduce accumulation in the basins. Traps that are too deep actually increase accumulation in the basins. A sill has proven to be the best measure for both mechanisms. If overdepth is desirable for navigation a shallow sediment trap is advised. This leads to a reduction of accumulation in the harbour basins for both erosion and fluid mud scenarios.

The Rhine Region of Fresh Water Influence (ROFI) is a shallow frictional river plume in front of the Dutch coast. Each tidal cycle a new tidal plume front with fresh-water is released. Recently, internal gravity waves have been observed in this plume. Using a Froude number analysis, support for the internal wave generation mechanism by a tidal plume front is found. It is shown, that on averaged neap tides the density stratification is large. This results in a larger area where the internal waves can be released from the tidal plume fronts compared to spring tides. As the Rhine ROFI is located in shallow water, it is investigated what the effect of bathymetry variation is on internal waves. This is studied by extending the standard KdV model derivation to account for a variable bed. This resulted in a small correction on the propagation speed inside the KdV equation. Observations of internal waves have been used to validate the KdV model. By scaling analysis of the observed waves it is obtained that the relative wave height and relative depth balance for most of the observed events. For these events the wave period and velocity amplitude of the KdV model are well matched with the measurements. This showed that the KdV model may be used for a first estimate of internal waves in the Rhine ROFI. By developing a TGE fitting procedure, it was possible to obtain the pycnocline depth and the direction of wave propagation with only limited data available. Therefore, the parameters have been varied and the error between the TGE solution and the velocity potential obtained from the velocity measurements has been minimized.

Phenomena like sea level rise, global warming and erosion together contribute to increasing flood risk in vulnerable coastal areas. As this flood risk increases, initiatives to mitigate the effects of climate change in the coastal zone are also increasingly sought. During recent years, the view that these measures should be circular has gained significant momentum. In line with this, the idea that sediment should not be treated as waste, but as a valuable product in a circular economy has been widely accepted. Within this theme, the sediment uses as resources in circular and in territorial economies (SURICATES) was created to develop and execute eco-innovative solutions for the reuse of sediments in Western Europe. As a part of SURICATES, over the course of a nine week pilot, a total of 500 tonnes of sediment was reallocated in a designated area in the Rotterdam Waterway, with the expectation that this sediment would be transported out of the Rhine-Meuse estuary into the North Sea. The SURICATES project is one of the first real large-scale efforts to reuse sediment for economic as well as ecosystem services. Effective implementation of the SURICATES project, however, requires a thorough understanding of the governing physical processes impacting the distribution of the deposited sediment locally. Furthermore, to assess the feasibility of similar future applications, efficient modelling of the pilot project is necessary. The work presented here aims to elucidate the hydrodynamic processes that are governing in the Rotterdam Waterway, within the framework of the SURICATES pilot project, and assess the reproducibility of these processes by (two) predictive models that are currently operational at the Port of Rotterdam. A special 6-hour monitoring survey was set up to measure salinities, velocities, temperature, and suspended particulate matter (SPM) along a transect crossing the reallocation location. In combination with a literature review, this dataset provides the basis for research into the predictive capabilities of two currently operational hydrodynamic models. Analysis of this dataset reveals the dominant terms in the momentum balance, the influence of Coriolis, the occurrence of internal waves, and the effect that all these mechanisms may have on the SPM distribution around the reallocation location. When the system dynamics are elucidated, the model performance of the two hydrodynamic models is assessed—both quantitatively and qualitatively. It is also investigated whether phase shifts are introduced in the models. It is found that the primary hydrodynamic processes in the Rotterdam Waterway are related to the barotropic tidal asymmetry imposed at the river mouth, the tidal excursion of the salt wedge, baroclinic exchange flow processes, and turbulence damping at the pycnocline. Turbulence damping at the pycnocline generally poses an upper limit to the (re)distribution of SPM over the water column, although field data suggests that this damping may not be sufficient to counteract diffusion processes locally. This effect occurs under certain forcing conditions and during low water slack. Furthermore, an internal Froude number analysis provides evidence for the possible generation of internal waves in one of the river’s bends. The evaluated models, however, are not capable of reproducing all of these hydrodynamic processes adequately. Although both models adequately reproduce water levels and the vertical velocity structure, they have difficulties predicting the pycnocline height. Additionally, it is found that both models introduce a small phase shift in the velocity and salinity prediction. The research presented here is a contribution to the understanding of the governing hydrodynamic processes in the Rotterdam Waterway, and the effect that (in)accurate modelling of these processes may have on future studies. Recommendations following from this research could improve future modelling practices.

The port of Rotterdam is located within the Rhine-Meuse estuary where a substantial amount of fine sediment transport takes place. Therefore, the port of Rotterdam is subject to significant siltation, requiring maintenance dredging to guarantee a sufficient nautical depth of fairways and harbour basins. To optimise the dredging strategy in the port of Rotterdam, a pilot study has been carried out wherein sediment is reallocated in the Rotterdam Waterway, during ebb, instead of offshore in the North Sea. Between May and November 2019, 210,000 tons of sediment has been reallocated. This pilot study has been carried out in the context of the larger EU-Interreg Sediment Uses as Resources in Circular and Territorial Economies (SURICATES) project. The main goals are to re-use the sediment as a resource and to reduce the sailing time of the dredging vessels. Both ideas comply with the Building with Nature philosophy; a concept gaining popularity over recent years in The Netherlands focusing on, amongst others the optimisation of dredging strategies. It is expected that the reallocated sediment is mainly transported offshore, while at the same time some of the sediment will nourish the river banks of the Rotterdam Waterway enhancing its flood resilience. This thesis focuses on understanding the fine sediment behaviour of the SURICATES pilot project on two different scales. This is done by analysing measurements and model hindcasts. The measurement campaign is set-up by Deltares and the Port of Rotterdam. For the model hindcasts an operational hydrodynamic and sediment model is used. On the small scale this is done by focusing on the behaviour of a single disposal over a tidal cycle. The large scale focuses on the cumulative long term behaviour of all sediment reallocations. For the small scale two measurement surveys are analysed. In both surveys it is found that a sediment reallocation executed by bow coupling is subject to mixing up to halfway the water column. Subsequently, the sediment plume is advected around and below the pycnocline. Further measurements in the mid field are lacking, but it is hypothesised that the majority of the sediment settles during subsequent low water slack. For the other execution method, drawing the bottom doors, which is used to reallocate the majority of the sediment, useful measurements are absent. It is hypothesised that the majority of this reallocated sediment is confined in the salt wedge and therefore mainly transported upstream over time. To assess the long term behaviour of the cumulative behaviour of all sediment reallocations, a different measurement campaign is set-up. In this measurement campaign, bed samples are collected prior to and during the pilot study to determine the change of the bed composition. In this campaign an indication for increased sedimentation related to the pilot study is found for nearly all the sample locations. The short term model study is set-up to enhance the understanding of the short term behaviour of a sediment plume, to derive an accurate source term for the sediment disposals and to carry out a sensitivity analysis. This sensitivity analysis is executed to derive the influence of differences in disposal method, timing of disposal, and uncertainties in the model. It is found that the execution method has the largest influence on the critical sediment fluxes on the short term, followed by the timing of disposal. From the long term model hindcast, in which the entire pilot study is hindcasted, it is found that 27% of the total amount of reallocated sediment flows downstream from the location of disposal and 73% upstream. These estimations are in line with the hypothesis and long term measurement results, but a thorough calibration of the results is lacking. To conclude, in this thesis a pilot study utilising a different sediment reallocation strategy in the port of Rotterdam has been investigated. This study shows that majority of the sediment disposed, in the current set-up of the pilot study, is estimated to flow upstream. In the sensitivity analysis, it is predicted that this might be caused by the timing of disposal or method of execution. It is also found that the initial behaviour of the sediment plume and the long term measurement contain a large amount of uncertainties. As most important recommendation for future work an expansion of the current measurement survey is proposed with at least two fixed locations: one downstream and one upstream of the location of disposal. In this way sediment fluxes can be established, which can also be used to verify and calibrate the sediment model.

The amount of suspended sediment spill released during dredging activities in the Fehmarnbelt strait is monitored along the excavated trench to prevent negative effects on local ecology. Stratification due to the interaction of saline water from the North Sea and fresh water from the Baltic Sea forces bi-directional flow of the layer above and below the density gradient, causing bi-directional spread of the dredging plume perpendicular to the trench as well. During such an event, monitoring on both sides of the trench is required. By mapping out the spatial and temporal behaviour of stratification, a prediction can be given on where and when measuring on both sides of the trench will be needed to include the baroclinic effect. Figures created with monitoring data show that the density profile is influenced by the salinity, rather than the temperature. Therefore, stratification predominantly depends on the in and outflow of water with respect to the Baltic Sea. The figures also show a larger density gradient during out than inflow. It can also be observed that where the water depth is restricted to 10 meters, wind and bottom friction mix the entire water column. Therefore, stratification occurs predominantly during outflow in sections deeper than 10 meters, indicating the need for monitoring the bi-directional plume spread during such circumstances. Whether stratification occurs during inflow in sections deeper than 10 meters likely depends on the duration and strength of the wind forcing and the initial strength of the density gradient prior to the inflow event. Further analysis should be done to confirm this. Signs of Ekman transport, return flows and the deflection of the currents towards deeper water can also be observed in the measurement figures. Since these processes affect the plume spread direction, additional research can be done on the behaviour of the current direction in the Fehmarnbelt.