Anthropogenic influences have disproportionally affected freshwater ecosystems, and a loss of biodiversity is forecasted to greatly reduce ecosystem function and services. Loss of species may destabilize communities by limiting the stabilizing forces of compensatory dynamics and/or statistical averaging, both of which are effects that can buffer variation in aggregate community properties. Currently, support for positive diversity-stability relationships stems from experiments with simple communities at small spatial and temporal scales, and application to natural communities is limited. Using a long-term dataset of 35 stream fish communities matched with hydrologic data, we show that community stability (annual variation of standing biomass of fishes) was less variable in more species-rich communities and was not associated with stream hydrology. Only the statistical averaging model of community stability was consistent with observed patterns of lower biomass variation in more species-rich communities. Our findings suggest anthropogenically induced extirpation of vertebrate consumers may lower community biomass stability in complex ecosystems.