A multitrophic model integrating the effects of flooding disturbance and food web interactions in rivers predicted that removing floods would cause increases of predator-resistant grazing insects, which would divert energy away from the food chain leading to predatory fish. Experimental manipulations of predator-resistant grazers and top predators, and large-scale comparisons of regulated and unregulated rivers, verified the model predictions. Thus, multitrophic models can successfully synthesize a variety of ecological processes, and conservation programs may benefit by taking a food web perspective instead of concentrating on a single species.