In this thesis, I reproduced fine sediment dynamics in the complex geometry San Francisco Bay- Delta estuarine system using the flexible mesh, process-based model, Delft3D FM. Based on solving the hydrodynamic shallow water equations and the advection-diffusion equation for sediment, the model allows for describing the spatial and temporal variability of suspended sediment concentration (SSC), which is subsequently translated into turbidity levels, deposition patterns, sediment budgets and coupling with ecological and contaminants models. We applied the model at a long-term, system scale as well as a seasonal, local slough scale. The main forcing determining the sediment dynamics distinguishes these two scales. Temporal, high river flow is the main sediment dynamic driver in the Sacramento-San Joaquin Delta, which is called here an event-driven estuary. The Alviso Slough main sediment driver is tidal forcing, therefore, referred to as a tide-driven estuary.