San Francisco Estuary and Watershed Science

The delta smelt is a small, endemic fish that resides in the upper San Francisco Estuary. They are listed under state and federal Endangered Species Acts. Since 2002, their abundance has been at record low levels. Delta smelt are entrained at state (Banks) and federal (Jones) pumping plants that export water to much of California. Export cutbacks to limit entrainment have been controversial, making delta smelt arguably the most important fish in California. Kimmerer (2008) published the first estimates of proportional entrainment (mortality relative to population size) of delta smelt at the water export pumping plants, improving on previous estimates of absolute numbers entrained. This paper comments on Kimmerer’s estimates, which ranged from 0% to 40% annually with considerable uncertainty reflecting the challenge in estimating the distribution and numbers of this scarce fish. Kimmerer’s high estimates in some recent years and his conclusion that entrainment effects could be episodically important are counter to a lack of statistically significant correlation between entrainment and subsequent abundance. Analysis herein justifies estimates of lower proportional entrainment than suggested by Kimmerer. Based on alternative assumptions, his highest annual estimates of adult proportional entrainment would have been no more than 13% and could even be in the range of 5% to 10%. Most adjustments resulting from alternative assumptions underlying high estimates of larval-juvenile proportional entrainment cannot be quantified. However, it is argued here that eight of ten key assumptions underlying those estimates resulted in upward bias. Lower estimates of proportional entrainment would be consistent with the lack of statistically significant relationships between entrainment and subsequent abundance in previous studies and suggest that assessment of the importance of entrainment awaits additional analyses that narrow uncertainty. Findings of detection problems with adult and larval-juvenile surveys suggest adding more stations and other adjustments to resolve these problems.