Executive Summary 
A proposed approach that could be used by the State to develop nutrient criteria for the 
Yaquina Estuary, Oregon is presented. The approach is based on a synthesis of research results 
derived from field sampling at multiple temporal and spatial scales, assembling data to construct 
historical trends in water quality parameters, and a variety of modeling approaches. 
Yaquina Estuary is a small, drowned, river valley estuary located along the central 
Oregon coast. Approximately 48% of the estuarine area is intertidal. The designated uses within 
the Yaquina Estuary and River include aquatic life harvesting (shellfish growing and fishing), 
agricultural (livestock watering), municipal (public water supply), recreation (water contact 
recreation), ecological (resident fish and aquatic life, salmonid spawning and rearing, 
anadromous fish passage) and aesthetics. 
Spatial and temporal variability in water quality indicators were assessed for multiple 
water quality parameters, including nitrogen, phosphorus, chlorophyll a , dissolved oxygen, total 
suspended solids, and water column light attenuation. Spatial scales examined included variation 
within the Yaquina Estuary, as well as comparison of some parameters to short term studies of 
six additional Oregon estuaries, and comparison to a single sampling of 14 additional Oregon 
estuaries conducted by the US EPA National Coastal Assessment program. Green macroalgal 
occurrence was evaluated to determine whether this was an appropriate indicator for nutrient 
responses within the Yaquina Estuary. Lower depth limits for the seagrass (Zostera marina ) 
were determined in order to estimate the minimum light requirements for sustaining seagrass. 
Field results were used to confirm output from a Seagrass Stressor-Response Model. 
Because there were limited data for applying the reference condition approach for the 
class of estuaries similar to the Yaquina Estuary, we used in situ observations within Yaquina 
Estuary as a basis for determining an Estuarine Reference Condition. Cumulative distribution 
functions (CDFs) were produced for water quality variables for the Yaquina Estuary and 
compared to CDFs for other Oregon estuaries using two independent data sets. Key percentiles 
(25 th , 50 th , 75 th ) for water quality parameters were used as inputs to a Seagrass Stressor-Response 
Model to determine whether particular percentile values would be adequately protective of 
seagrass within the Yaquina Estuary. 
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