Estuaries are dynamic partially enclosed water bodies that are constantly or periodically influenced by the ocean and at least occasionally impacted by river discharge. This creates unique but fragile ecosystems that have to be managed with care in order to be recreationally, economically and ecologically valuable. One of the management issues is water quality, which is mainly influenced by hydrodynamic processes and other processes affecting the transport of dissolved or suspended materials. The understanding of the hydrodynamic processes of an estuary and its physical drivers is crucial for management. One of these fragile ecosystems that have been prone to many human interventions in the past, is the Leschenault Estuary. In this thesis, a 3D-numerical model is developed in D-Flow FM to unravel the governing hydrodynamics of the Leschenault Estuary. Besides, field measurements provided data used as input for the numerical model and more information about the dynamics of the Leschenault Estuary. Most importantly, a methodology is proposed to improve the efficiency in drawing relevant conclusions from observed and modelled data. Efficient and easy-to-apply classification methods are therefore considered that could be powerful management tools. To validate this methodology, a scenario has been considered where the Preston River is aligned to the Bunbury Port. The governing hydrodynamic processes in the Leschenault Estuary are internal circulation, stratification and turbulence, which are predominantly driven by the freshwater discharge and the tides. However, the dominant physical processes are highly dependent on the seasonal conditions and the specific locations. In general, three different seasonal conditions were distinguished: normal summer, normal winter and peak river discharge conditions. In summer, freshwater discharge is reduced, which increased the impact of tidal stirring and vertical mixing. In winter, the high river flow generated more stratified flows and under peak discharge conditions some areas of the estuary presented salt-wedge regimes. The Leschenault Estuary can be spatially subdivided in four distinct regions (southern, central, northern and riverine basin), based on the governing hydrodynamic processes. The southern basin is the most dynamic and can not be specified by a single regime due to the influence of the ocean, the Preston River, the Collie River and the northern regions. The central and northern basins were classified as partially-mixed throughout the year and showed weakly to strongly stratified water bodies, depending on the seasonal conditions. Furthermore, a classical estuarine circulation develops under normal winter conditions. In summer, the northern regions become hypersaline, generating an inverse circulation in the central and northern basins. The Collie River is characterized by a partially-mixed water body, with high stratification. Under peak discharge conditions, the salt wedge can be temporally forced out of the river and partially out of the estuary. Winds, waves and Coriolis have a significant influence on the hydrodynamics of the central and northern basin, due to their shallow and stagnant waters. The driving forces of the salt transport were obtained by the decomposition of the salt flux. The main physical processes affecting the salt transport between the estuary and the ocean along the transect of the 'Cut' over the whole year and in winter were freshwater discharge, topographic trapping and Stokes drift. Stokes drift was dominant in summer, followed by freshwater discharge and topographic trapping. This indicates that regardless the season the advective terms were dominant drivers of the salt transport. It also indicates the seasonality of the salt flux at the 'Cut'. The dominant salt flux components at the central basin was the Stokes drift, followed by freshwater discharge and topographic trapping. The Preston River alignment was compared with its current location to provide useful information for management and to evaluate the efficacy of the adopted classification methods. The scenario results were significantly different than the initial model results and the Preston River alignment had a substantial impact on the hydrodynamics of the Bunbury Port and the southern basin. Bunbury Port circulation became more stratified and its seasonal variation was increased, while the southern basin became less dynamic and partially-mixed, with low to high stratification. The Collie River and central and northern basins however remained almost unaffected. Further, the physical drivers of the salt transport did not vary much but the role of the Stokes drift became relatively more pronounced at the `Cut', due to the decreased influence of freshwater discharge and topographic trapping. At the central basin, the Preston River alignment had a negligible effect on the physical drivers of the salt transport. However, larger spatial and temporal variability of salinity and temperature distributions were observed. It is therefore recommended to conduct an additional ecological valuation of this intervention. Valuable insights were presented in this thesis that have been critically validated. The used methods have proven to be efficient and valuable tools for management.

An increasing amount of the worlds coastal regions suffer from structural erosion due to anthropogenic influences. A prime example for this phenomenon is the Oosterschelde, Netherlands, where the partial closure of an estuary lead to a decline of the local intertidal flats, threatening the valuable functions they provide as an ecosystem and for shore protection. A sustainable measure to slow down the decline, is the usage of wave disrupting oyster reefs, which reduce the wave energy on the flat, thus reducing erosion. As of now, the conditionality and extend of the wave attenuation effect of such reefs is still widely unknown. This is thwarting a more extensive usage of oyster reefs for erosion management, since the actual effects of such a reef are highly uncertain prior to construction. This thesis was designed to investigate and quantify wave attenuation capabilities of an artificial oyster reef in a macrotidal environment, improving the understanding of the impact of such structures on their physical environment. A wave analysis was carried out on a reef using field data, allowing for the quantification of attenuation, the identification of processes, a parameterization of the results and an insight on the predictability of attenuation. Extensive field data was acquired on seven locations on a transect over the investigated reef, including pressure and velocity data. The reef was built using shell filled wire gabions and is orientated perpendicular to the main wind direction. It has dimensions of approximately 120 m length, 8 m width and 0.8 m height. The reef crest is located 0.5 m above mean low water level and 2.3 m below mean high water level, being emerged approximately 30 % of the time. Incoming waves are characterized by maximum significant wave heights of 0.8 m and maximum mean periods of 3 seconds. Wave attenuation was quantified by comparing the energy flux in front of (seaward) and behind (shoreward) the reef under different hydrodynamic conditions. The conditionality of attenuation was found to be best represented by the relative submergence ds /Hm0,i , which represents the ratio of the freeboard on top of the reef and the incoming wave height. Attenuation was found until a ds /Hm0,i ratio of approximately 4. Compared to the bare tidal flat in front of the reef, the reef attenuated energy up to 40 times more effectively per distance. The spatial footprint of the reef was found to vary strongly with different ds /Hm0,i ratios, but being roughly of the same order of magnitude as the reef length. Reflection, overtopping, wave breaking and friction were identified as the main mechanisms behind energy attenuation. An attempt to parameterize these was done using dimensionless numbers, which can be used to predict attenuation by using incoming wave, and reef characteristics. The determined processes were best represented by the parameters ds /Hm0,i and L01 /ds. Three empirical relations describing wave attenuation over breakwaters were used to investigate whether existing formulas can predict wave attenuation over the observed oyster reef. The measured and calculated results show a strong correlation of R ~ 0.9 but need to be tuned to reach reasonable root mean square errors. This implies that such existing formulas can be adjusted to represent oyster reefs, making them a possible tool to predict oyster reef performance in the future. The findings show that the present oyster reef is effective in attenuating waves and contribute to the overall understanding of how oyster reefs can reduce erosion. A better insight on the quantity of attenuation and the spatial footprint of the reef's effects was achieved. The footprint of the reef's effect is hereby limited to an area close to it, meaning that the reefs impact on erosion should not be overestimated. Such a reef should thus rather be seen as a complementary measure against erosion, stabilising the local area. As a next step, setting up a numerical model is recommended, where the wave attenuation can be linked to actual erosion quantities. Quantitative research on additional oyster gabions can further be used to refine existing empirical relations, creating some predictability of transmission values over oyster reefs.