Nutrient perturbations are a threat to aquatic ecosystems worldwide. Interactions among important species can influence the recovery of aquatic ecosystems from nutrient perturbations, and the persistence in a clear water state for a given regime of nutrient loading. In a factorial manipulation of two foundation species (macrophytes and mussels), we measured 16 large (15000L) ponds at high resolution (15 min interval) over two years with two periods of nutrient perturbation. We found that each foundation species had strong individual effects on multiple ecosystem properties (e.g. phytoplankton densities and metabolism), largely in line with our expectations (i.e. reduction of algal biomass relative to control). However, when both species were present, we saw dramatic increases in algal biomass and other ecosystem parameters, indicating strong non-additive antagonistic effects. Overall, our results demonstrate how interactions between foundation species can cause surprisingly strong deviations from the expected responses of aquatic ecosystems to nutrient additions.