Allelopathy is common mediator of ecological interactions wherein an organism produces a chemical harmful to the success of heterospecifics. While allelochemicals have direct effects on bipartite interactions, they may also cause ecological indirect effects where a third player mediates the suppression of competitors or is indirectly impacted by the chemical. Herbivores are likely to encounter indirect effects through consumptive interactions with target plant species that may be reduced in quantity (density-mediated) or quality (trait-mediated) by a plant competitor’s allelochemical. We addressed how such indirect effects may occur across a range of microcystin concentrations, an allelopathic chemical of increasing concern in freshwater systems produced by harmful algal blooms. We found that microcystin not only had direct effects on the growth of a plant competitor, the duckweed Spirodela polyrhiza, but also indirect effects on the aphid herbivore Rhopalosiphum nymphaeae. Aphids experienced a negative impact of microcystin concentration on growth that was mediated by duckweed quality. We also tested for direct and indirect evolutionary effects and found that microcystin exposure had a marginal indirect effect on changes in aphid genotypic frequency. Our results indicate the need to consider indirect effects and trait mediation in community dynamics and evolution in the presence of allelochemicals.