7. 
Chlorophyll a as a Water Quality Response Measure 
7.1 Seasonal, Zonal, and Long-Term Trends in Chlorophyll a 
Chlorophyll a is often used as a surrogate for phytoplankton biomass and as an indicator of 
trophic status in eutrophication assessments (Bricker et al., 1999). There were seasonal differences in 
water column chlorophyll a in the estuary. Peak chlorophyll a levels occurred during the months of 
June to August (Figure 7.1). Seasonal chlorophyll a patterns were likely related to light limitation and 
flushing (as discussed in Section 5.2). The median wet season chlorophyll a was 1.6 pg f 1 (n = 293), 
while during the dry season the median increased to 4.9 pg F 1 (n = 1205). Dry season chlorophyll a 
levels in Zone 2 (Median = 5.3 pg F 1 , n = 229) were significantly higher than those in Zone 1 (Median 
= 3.3 pg F 1 , n = 347; Mann Whitney Rank Sum, p<0.001). During the late spring, there have been 
recurrent non-toxic red tide blooms of Myrionecta rubra in the vicinity of Toledo. During the dry 
season, chlorophyll a concentrations occasionally reached 15 pg F 1 in the vicinity of Toledo (8% of the 
recent observations). In the tidal fresh portion of the estuary, there were recurrent algal blooms during 
June and July, with chlorophyll a concentrations reaching 80 pg F 1 . 
There are limited historical data to assess long-term trends in chlorophyll a. Comparison of 
historic (1973-1983) and recent (2000-2006) chlorophyll a levels during the dry season reveal that 
there has been a decline in median chlorophyll a levels in both zones (Figure 7.2); although these 
declines are statistically significant (Mann Whitney Rank Sum, p< 0.001) they do not indicate a shift in 
trophic status of the estuary. There was a statistically significant decreasing trend in dry season 
chlorophyll a in Zone 1 (Mann Kendall, p<0.001), while in Zone 2 there was no significant trend. The 
changes in chlorophyll a that occurred in the Yaquina Estuary are small in magnitude (1 pg F 1 ) 
compared to changes that have occurred in other estuaries (Cloem, 2001; Harding and Perry, 1997). 
For example, in Chesapeake Bay chlorophyll a levels increased 5- to 10-fold in the lower portion of 
the estuary during the interval of 1950-1994 (Harding and Perry, 1997). A statistically significant 
zonal difference in chlorophyll a levels (Zone 2 higher than Zone 1) is present in the historic data as 
well as the recent data (Mann Whitney Rank Sum, p < 0.001). Peak chlorophyll a levels in Zone 1 
appear to be higher in the recent data compared to the historic; however, this is probably an artifact of 
sampling frequency. Blooms imported into Zone 1 from the coastal ocean are episodic in nature, 
reflecting the variability in wind forcing. Peak chlorophyll a levels in Zone 2 are similar for the 
historic and recent data. 
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