The relative importance of top-down invader effects relative to environmental drivers was determined by sampling crustacean zooplankton, rotifer, and phytoplankton communities in a set of invaded and noninvaded reference lakes. The non-native invertebrate predator Bythotrephes had significant effects on zooplankton community size structure, rotifers, and phytoplankton taxonomic composition, but no significant effects on crustacean zooplankton taxonomic and functional group composition. Part of the variation in phytoplankton communities was explained by the presence of the invader. Because Bythotrephes is generally known to be a carnivore and to not consume phytoplankton, this effect is likely mediated by the zooplankton community’s response to environmental gradients. Although Bythotrephes appears to indirectly alter phytoplankton composition in invaded lakes, there was no evidence of a trophic cascade, and edible phytoplankton biovolume did not increase in invaded lakes. These complex direct and indirect interactions suggest that effects of invaders may be highly context-dependent, and therefore pose a significant challenge for predicting wider community and ecosystem responses.