12.3 Model Simulations and Input Data 
The SRM was used in a heuristic fashion with idealized input data. Composite temperature and 
salinity time series were generated using YSI datasonde data from two stations, one located in each 
zone (distances from mouth of the estuary of 3.7 and 17.9 km). The composite time series represented 
average conditions from 1999-2003. For the solar irradiance, a composite incident photosynthetically 
active radiation (PAR) time series was generated using data collected by WED during 1999-2003 
(Appendix Figure E.2). This PAR time series represents average incident light conditions (I 0 ) in the 
study area at 15 minute intervals for the year. The underwater light environment used in the model 
includes daily variations in surface irradiance with the addition of tidal variations in water surface 
elevation, and zonal and seasonal differences in water clarity ( k ). The underwater light environment 
was simulated for each zone as 
/ ( z /=i,...,« > A 0 = 1 o (0 e ~ kjS (Zi +h) 
where j represents the zone, z, represents the depth (relative to MLLW), h is tidal variation in water 
surface elevation, and kjs is the diffuse light attenuation coefficient for the specific zone (j) and season 
( S ), which were obtained from the percentile analysis calculated using the continuous Yaquina Estuary 
data set (Table 9.1). Tidal variations in water surface elevation (/?) were incorporated using hourly 
water level data from a tide gauge in Zone 1 (http://tidesandcurrents.noaa.gov7. Station 9435380 South 
Beach). 
Table 12.1 Input data from percentile approach for different SRM simulations. . 
Case 
Zone 
Dry Season 
Wet Season 
kd , nf 1 
DIN, pM 
kd , nf 1 
DIN, pM 
1 
(Median) 
1 
0.78 
14.1 
0.74 
11.6 
2 
1.53 
13.7 
1.20 
55.0 
2 
(25 th %) 
1 
0.62 
8.3 
0.55 
6.8 
2 
1.14 
7.3 
0.97 
30.7 
3 
(75 th %) 
1 
1.00 
20.4 
0.89 
19.1 
2 
2.26 
23.1 
1.54 
73.5 
Simulations were run for 3 cases, the median, 25 th , and the 75 th percentiles as representative of 
different levels of potential protective criteria for Yaquina Estuary. For these analyses, the estuary was 
divided spatially into a lower (Zone 1) and upper (Zone 2) region and temporally into a wet and dry 
season (Table 12.1). The transition from wet to dry season conditions for both kj and DIN 
90 
