14 estuaries ot the State. An additional 30 sites were sampled in Tillamook Bay to assess condition of 
this National Estuary Program system, and Tillamook Bay was thus not included in the sample 
selection tor the other 50 sites. Tributary estuaries of the Columbia River that are located within 
Oregon were included in the 1999 sampling effort, while the main channel area was not sampled until 
2000. In 1999, estuaries were divided into four strata based on size, and approximately equal sampling 
effort was placed in each stratum, to insure sampling across the entire estuarine size spectrum. The 
Oregon 2000 study included only the main channel area of the Columbia River, and was split into two 
strata, the lower, saline portion and the upper, freshwater portion, with 20 and 30 sites sampled, 
respectively. Additional samples were obtained in the WA tributary estuaries of the Columbia River in 
1999, but were not included in the data presented in this section. A total of 128 out of the 130 target 
stations were successfully sampled for water quality indicators. 
4.4 Percentile Approach 
Previous assessments of water quality conditions in PNW estuaries were hindered by the 
limited availability of water quality data for estuaries in the region, particularly in Oregon (Bricker et 
al., 1999). Since 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 the Estuarine Reference Condition (as recommended by U.S. EPA, 2001). To accomplish 
this, we produced cumulative distribution functions (CDFs) for the Yaquina Estuary and compared 
those to CDFs of other Oregon estuaries using two independent data sets (Classification Study and 
NCA for Oregon estuaries). The NCA and Classification data sets were sampled at different temporal 
and spatial scales. The Classification data set used in our analyses included samples from six estuaries, 
with 10-17 stations sampled per estuary during both flood and ebb tidal conditions. Data from the 
Yaquina Estuary collected as part of the Classification Study were not included in the computation of 
percentiles for this data set. The NCA data set sampled 14 Oregon estuaries. The number of stations 
in each estuary was randomly determined within an estuarine size stratum. Timing of sample 
collection with respect to tidal stage was random. The number of sampling locations per estuarine 
system in the NCA data set ranged from 1 (Alsea and Yachats) to 67 (Columbia). 
In Appendix C, we present various classifications of the estuaries in the Classification Study 
and NCA data sets based upon geomorphology, susceptibility to nutrient pollution, and statistical 
clustering of physical and hydrologic variables. The number of classes ot estuaries (or types) depends 
n 
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