Estuaries are partially enclosed water bodies where river water mixes with sea water. Estuaries provide important ecological functions which are strongly regulated by estuarine hydrodynamics and sediment dynamics, and also by human interventions. Sustainable management of such systems therefore requires a thorough understanding of the interplay between hydrodynamics, sediment dynamics, and human interventions. However, estuaries are often complex systems influenced by river runoff and coastal hydrodynamics (tide, wind, and wave), which all interact with human interventions on various time and spatial scales. Our understanding of estuaries is still insufficient to understand the response of strongly engineered systems to both human interventions and to natural fluctuations. Many estuaries worldwide are strongly influenced by a wide range of human interventions, including engineering constructions, deepening, and land reclamations. An example of highly engineered estuaries is the Changjiang Estuary (CE), China. The upstream river discharge and sediment load is strongly influenced by the Three Gorges Dam (TGD), a multi-purpose dam in the Changjiang River aiming at optimizing flood control and irrigation, and generate hydropower. In the North Passage (NP), an outlet and the main navigation channel of the CE, the Deepwater Navigation Channel (DNC) has been constructed to improve channel navigability. The DNC project includes constructions of dikes and groynes, and regular dredging work. These various interventions strongly influence estuarine hydro- and sediment dynamics but take place concurrently, and therefore their individual impact is not straightforward to assess. A better understanding of the impact of these interventions requires systematic analysis of hydrodynamic and sediment transport processes in relation to the interventions. This dissertation aims to unravel the effect of groynes on lateral flows and sediment transport in a tidal channel-shoal system (i.e. the NP). Groyne fields provide buffer zones, with a salinity lagging behind that in the main navigation channel. The resulting lateral salinity gradients drive lateral density currents, which in turn modify longitudinal salinity gradients in the main channel. These salinity-driven currents also impact the lateral sediment exchange between the main channel and the groyne fields. The effects of groynes on lateral flows and lateral sediment exchange are analyzed using numerical simulations in combination with in-situ observations. Water-bed sediment exchange processes are investigated in more detail using measurements collected with two tripods deployed in the CE. Measured bed level changes are analyzed by semi-automatically fitting the Krone-Partheniades equations to the bed level data using observations of velocity and sediment concentration. This method provides continuous timeseries of sediment properties related to erosion and deposition. It is demonstrated that the erosion parameters are strongly fluctuating, and not constant as typically assumed in numerical models. Such a variability needs to be reflected in a model, either by time-varying parameters or including more detailed processes (for example, consolidation). This dissertation introduces a method to obtain a parameter space that includes the values and accuracies of all potential combinations of input parameters, which is important input for morphodynamic models. To further quantify effects of groynes on hydrodynamics and sediment dynamics, an idealized hydrodynamic model with a single channel with groynes is developed and analyzed. The idealized system has geometric features comparable to the NP, but is set up in such a way that the groyne field aspect ratios (the ratio of the distance between contiguous groynes to the length of groynes) can be systematically investigated. Model results reveal that groynes can influence channel hydrodynamics and local mixing conditions, which influence lateral flows and the longitudinal salt intrusion. Salt intrusion is highest for intermediate aspect ratios, but weaker for very wide or narrow groyne fields. These results highlight the complexity of the hydrodynamics in salt fresh-water transition zones, and specifically the role of human intervention thereon.