Copper is acutely toxic to, and directly affects, primary producers and decomposers, which are key players in essential processes such as the nutrient cycle in freshwater ecosystems. Even though the indirect effects of metals (for example effects due to changes in species interactions) may be more common than direct effects, little is known about the indirect effects of copper on primary producers and decomposers. The effects of copper on phytoplankton, macrophytes, periphyton and organic matter decomposition in an outdoor lentic mesocosm facility were assessed, and links between the responses examined. Copper directly decreased macrophyte growth, subsurface organic matter decomposition, and the potential for high phytoplankton Chlorophyll a concentrations. However, periphyton cover and organic matter decomposition on the surface of the sediment were stimulated by the presence of copper. These latter responses were attributed to indirect effects, due to a reduction in grazing pressure from snails, particularly Physa acuta, in the higher copper-contaminated mesocosms. This permitted the growth of periphyton and other heterotrophs, ultimately increasing decomposition at the sediment surface. The present study demonstrates the pronounced influence indirect effects may have on ecological function, findings that may not be observed in traditional laboratory studies (which utilize single species or simplistic communities).