A Three-dimensional Water Quality Model for Estuary Environments

Estuary environments are one of the least studied, but most threatened ecosystems on the planet. Decades of human interaction and alteration of estuaries have lead to the degradation of these vital ecosystems, and many estuaries worldwide require immediate management strategies to mitigate the damage. One of the only unifying characteristics of all estuaries is their location at the interface between land and sea. Estuaries drain large watersheds and as such mediate a large flux of flow, sediments and nutrients from the land and rivers to the oceans and means these ecosystems are subject to a number of important physical forces, including river flow, tidal energy and wind forces. This temporal and spatial variability produces a set of biogeochemical factors unique to each estuary, and understanding the causes and possible solutions for problems that arise in estuaries requires a complete understanding of these interacting factors.;In order to alleviate the challenge facing estuaries, it is critical to understand how the physical and biological processes interact. Although a great wealth of information can be gathered from fieldwork, to investigate future solutions an efficient computer model that can capture the most important processes occurring in the system is vital. In the case of estuary systems where the interacting forces (wind, tides, river and salinity and temperature induced stratification) are complex and unsteady, a three-dimensional model is necessary. In this study, a three-dimensional water quality model (SI3DWQ) is developed as a coupled model to an existing hydrodynamic model (SI3D). The water quality modules added to the model use velocity, water depth and water temperature information solved in the hydrodynamic module to simulate the advective and diffusive transport of a number of constituents, including: dissolved oxygen, nitrogen species, phosphorus species, phytoplankton as chlorophyll-a, suspended sediment, and conservative and non-conservative tracers.;After development of the water quality module, SI3DWQ was used to investigate water quality problems facing the San Francisco Bay Estuary. The first two apply the model to the Stockton Deep Water Ship Channel (DWSC), a stretch of the San Joaquin River that has been subject to low dissolved oxygen concentrations since the 1960s. The model was first calibrated to a SF6 tracer study to determine the transport dynamics in the DWSC. The tracer modeling study revealed the importance of the turning basin, especially at low river flows in the residence time of the DWSC. After completion of the tracer study, the water quality model application to the DWSC was expanded to include phytoplankton, nitrogen and phosphorus species and dissolved oxygen to investigate the important physical and biogeochemical processes contributing to low dissolved oxygen in the reach. The model application identified the importance of stratification processes in the dissolved oxygen concentrations and highlighted the importance of the turning basin in the mixing dynamics of the entire system. These model applications can be used to help guide management decisions for the San Joaquin River and DWSC.;The last application of the model uses SI3D to simulate a hypothetical permanently flooded Delta island and the surrounding channels to determine the potential effects of geometric characteristics of a flooded island in the Delta on its biological productivity and establishing hydrodynamic and water quality background for scientifically based habitat restoration. The results identify several points to consider in managing future permanently flooded Delta islands: (1) a flooded Delta island can either be a sink of chlorophyll-a or produce population levels that support secondary production; (2) depth of a flooded island is important, with shallower (3m and 4m) subsided islands supporting larger populations of phytoplankton; (3) two island breaches export higher concentrations of phytoplankton than single-breached polders; (4) islands oriented perpendicular to the channel support greater concentrations and fluxes of chlorophyll.;The results from the modeling applications show that the newly developed SI3DWQ can successfully be used to investigate a wide range of water quality problems in estuaries. The results from the studies can be used by managers and policy makers in the San Francisco Bay Estuary to help guide decisions about the future of this complex system. The success of the model applications to the San Francisco Estuary suggests that the model can be applied to other estuaries worldwide to help determine solutions for these critical ecosystems.