In the Eel and other sunlit rivers, consumers derive most of their carbon from algae. Large algal blooms follow winter floods that scour away over-wintering armored grazers. Green Cladophora proliferations become overgrown by highly edible diatoms. Under very low summer base flows, however, cyanobacteria, some toxic, can smother Cladophora-diatom growths. Both diatoms and cyanotoxins are exported from the Eel to the coastal ocean. Riverine and likely marine salmonids in 3-4 link food chains feed on prey built of algal carbon. Following drought years with no flood scour, inedible armored grazers overwinter, then suppress algae, so predators are deprived of algal energy. These inferences from isotopic surveys, observations and field experiments are supported by diatom frustule counts in an 84-year stratigraphic record from the Eel’s marine canyon. All suggest that top-down effects of floods on algal blooms (grazer release) are stronger than bottom-up control (e.g. nutrient inputs). If summer droughts (and human water extraction) intensify under greenhouse warming, food chains could shorten further, from two to one trophic level, as hydrologic conditions favor toxic cyanobacteria, recently implicated in several dog deaths in the Eel River and sea otter deaths offshore.