In this project, three hydrodynamic models of the San Diego Bay were developed. The first one was a coarse model (2:5 km resolution) covering all of Southern California. This model affords valuable data for areas close to San Diego Bay, but is not capable of providing any information from within the bay itself. The second model is a standalone, high-resolution (50m) hydrodynamic model that is capable of simulating the hydrodynamics within the bay. However, this model is unaffected by the information from outside of the actual bay. The third is a multi-domain model of the San Diego Bay, which is a high-resolution model nested within the coarser model of Southern California. This model is capable of simulating the hydrodynamics within the bay, and enables the study of the impact of events originating well outside of the San Diego region; hence, it offers broader capabilities and applications. All three of these models can be used to study the San Diego Bay's ecology, including the effect of toxic pollutants and the overall water quality in the region. Considering the fact that the San Diego Bay is extremely important to both the economy and ecology of the region, and taking into account that the models developed here are based on free source code (Delft3D) and freely available data sets (making the operation costs very low), it becomes fairly certain that researchers, scientists, and institutions could benefit from the models developed in this project. As a result, this model could help the San Diego community better understand the local environment, thereby enabling it to make better, more informed decisions regarding projects affecting the ecology of the region.