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.