Yes. The Biological Opinion (basically, a permit from USFWS with conditions protective of delta smelt) accounts for that though, by varying allowable loss of delta smelt relative to the most-recent delta smelt abundance index.
Delta smelt are fragile. That's not an issue though, because there is no need to sample them downstream of the CVP and SWP south delta pumps. Salvage happens way upstream from the pumps and any fish that aren't salvaged are defined as lost.
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