Some models suggest that omnivory stabilizes food webs by increasing the number of trophic interactions. In aquatic systems, omnivorous fish that consume sedimented detritus may also confer stability by translocating a steady supply of nutrients. In a large-scale test of the omnivory-stability hypothesis in experimental ponds, phytoplankton biomass and species diversity were more resistant and resilient to nutrient pulses when omnivorous fish were abundant. However, omnivores destabilized phytoplankton community composition, which in response to the perturbation changed to a greater extent when omnivores were abundant. Indirect effects of omnivores on phytoplankton community composition, prior to perturbations, may be responsible for contrasting stability responses. Specifically, phytoplankton assemblages in ponds with low biomass of omnivores were dominated by the grazing-resistant chlorophyte Oocystis, possibly because of lower grazing rates by zooplankton at low omnivore biomass. Data on nutrient dynamics and phytoplankton stoichiometry suggest that Oocystis-dominated assemblages converted the nutrient pulse into new biomass more efficiently and rapidly than did assemblages dominated by other taxa. This rendered phytoplankton biomass in Oocystis-dominated assemblages more sensitive (i.e., less resistant and resilient) to nutrient pulse perturbations. However, in ponds already dominated by Oocystis before the nutrient pulse, Oocystis became proportionately more abundant after the pulse; thus, community composition changed relatively little. In contrast, in ponds with abundant omnivores, phytoplankton community composition changed greatly in response to the pulse, even though the response of phytoplankton biomass was relatively slight. Our results show that omnivory has complex effects on food web stability, mediated by species-specific interactions.