Although studies on biodiversity and ecosystem function are often framed within the context of anthropogenic change, a central question that remains is how important are direct vs. indirect (via changes in biodiversity) effects of anthropogenic stressors on ecosystem functions in multitrophic‐level communities. Here, we quantify the effects of the fungicide chlorothalonil on 34 species‐, 2 community‐ and 11 ecosystem‐level responses in a multitrophic‐level system. At ecologically relevant concentrations, chlorothalonil increased mortality of amphibians, gastropods, zooplankton, algae and a macrophyte (reducing taxonomic richness), reduced decomposition and water clarity and elevated dissolved oxygen and net primary productivity. These ecosystem effects were indirect and predictable based on changes in taxonomic richness. A path analysis suggests that chlorothalonil‐induced reductions in biodiversity and top‐down and bottom‐up effects facilitated algal blooms that shifted ecosystem functions. This work emphasises the need to re‐evaluate the safety of chlorothalonil and to further link anthropogenic‐induced changes in biodiversity to altered ecosystem functions.