Hydrodynamic and Nutrient Source Model 
All field and laboratory data used in the development of hydrodynamic and nutrient 
source model were collected in accordance with WED SOP's and QAPP’s. (Tables B.l and B.2). 
A two-dimensional, laterally-averaged hydrodynamic and water quality model (Cole and Wells 
2000) was used to simulate the transport of riverine, oceanic and wastewater treatment facility 
(WWTF) effluent dissolved inorganic nitrogen (DIN) sources. This model is well suited for 
long-narrow estuaries, such as Yaquina Bay, where there are minimal lateral variations in water 
column properties. U.S. EPA (2001) suggested that this model may be useful in the estuarine 
nutrient criteria development and has been used in developing estuarine Total Maximum Daily 
Loads (TMDLS). 
In the model simulations presented in this study, Yaquina Estuary was represented by 325 
longitudinal segments spaced approximately 100-m apart with each longitudinal segment having 
1-m vertical layers. The model domain extended about 37 km from the tidal fresh portion of the 
estuary at Elk City, Oregon to the mouth of the estuary. Model simulations were performed for 
the interval January 1 to October 1 of 2003 and 2004 and included tidal and wind forcing as well 
as freshwater inflow. Parameters simulated included water surface elevation, salinity, water 
temperature, and DIN. 
Model calibration is the process of determining model parameters that are appropriate for 
the specific study location and time interval being simulated. The model used in this study was 
calibrated through adjustment of friction coefficient, eddy viscosity, and eddy diffusivity. To 
assess the model performance at simulating the hydrodynamics, we compared simulated and 
observed water level variations at two locations in the estuary and salinity and water temperature 
at four locations utilizing data from the YSI datasondes. Since the datasondes used at these 
stations were not leveled in we could only compare relative water level fluctuations, not absolute 
water level (referenced to MLLW). In addition, temperature and salinity from the CTD cruises 
were compared to simulated values. The model was assessed by calculating the root mean 
square error between observed and predicted variables. 
Each nitrogen source, riverine (N river ), oceanic (N ocean ), and WWTF effluent was 
modeled as a separate component. The nitrogen sources were modeled as 
dN 
dt 
transport — pN 
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