We propose to quantify the three-dimensional circulation within Yaquina Bay Estuary and the coastal waters in the vicinity of the bay using a state-of-the-art hydrodynamic model, validated with field observations as well as from existing long-term datasets. The numerical model to be used is the open-source, three-dimensional, Finite Volume Coastal Ocean Model (FVCOM). FVCOM is specifically designed to simulate the circulation in estuaries with large tidal forcing, regions of wetting and drying (inter-tidal flats), strong and variable freshwater input, and complex geometry and bathymetry. The unstructured-grid formulation of the model allows complex coastlines to be smoothly matched and for horizontal resolution to be varied according to the complexity of the bathymetry and the scales of the circulation features that need to be resolved. The objectives of the model are to demonstrate how circulation patterns change under forcing conditions that vary on tidal, storm event, seasonal, and long-term (climate) time scales and how the circulation within the estuary and offshore coastal waters near the estuary mouth control the residence time of water-borne materials within the estuary and the exchange of materials between the estuary and the coastal ocean.
A series of surveys of the currents and salinity field of the estuary and bay mouth using the R/V Elakha are proposed to validate physical characteristics of the bay and its waters that will be the basis for the model. These surveys are designed to measure the detailed variations of currents and salinity over a tidal cycle along the estuary and offshore of the estuary in the vicinity of its mouth. Four tidal-cycle surveys per year are proposed in order to contrast the circulation and salinity variability during periods of high river flow in the winter and spring and low river flow in late summer. In addition to these surveys, groups within the Hatfield Marine Science Center (HMSC), including the Environmental Protection Agency, Oregon Department of Fish and Wildlife, and the National Oceanic and Atmospheric Administration, will be providing us with existing long-term datasets describing relevant features including the coastal bay and river waters, local topography, and environmental and developmental changes in the region.
A focus of this study will be to develop a model that is of use to researchers, including groups at HMSC, studying the ecology of the bay who have interest in transport and residence time of planktonic larvae, nutrients, sediment and pollutants as well as in understanding the sensitivity of the bay and estuary to seasonal and climate variability and factors such as fresh-water input and developmental changes. We are working closely with research groups at HMSC and Oregon State University to ensure that the parameters addressed by the model meet the needs of current research and monitoring activity.
We will also create a visual learning tool from the numerical simulations as a communication tool for researchers as well as to policy makers, resource managers and development planners who must ensure that water-quality remains high in the bay. Graphical displays of the simulations will be used to demonstrate how circulation controls the movements and dilution of materials introduced into the system and the time it takes for these materials to ultimately leave the bay and estuary.
A final component of this research project is to modify the circulation model for use as an interactive learning tool for understanding how and why currents vary within an estuary and the transport pathways of nutrients, sediment and pollutants that are introduced into estuarine waters. We hope that such an interactive presentation could be displayed at the HMSC Visitor Center to promote marine science education.

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