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.