Freshwaters are affected by various stressors, such as contamination and exotic species, and are among the most imperilled biological systems on the planet. Copper is amongst the most common metal contaminants in freshwater systems, and in Australia and elsewhere, European carp (Cyprinus carpio L.) are a widespread pest species. Copper and carp can both directly affect primary production and decomposition, which are critical and interrelated nutrient cycling processes and ecosystem services. The aim of this study was to explore the direct and indirect effects of Cu and carp individually, and together on primary production, (periphyton cover, chlorophyll a concentration and macrophyte growth), and organic matter (leaf litter and cotton strip) decomposition processes in a controlled, factorial experiment in outdoor experimental ponds. There were significant reductions in macrophyte growth and organic matter decomposition as a result of Cu alone, while chlorophyll a concentrations and periphyton cover remained similar in Cu treatments and controls, probably due to the low Cu concentration in the overlying water. Carp addition alone had a direct negative effect on the biomass of aquatic plants outside the protective cages but was associated with an increase in the biomass of aquatic plants inside the cages, periphyton cover and chlorophyll a concentrations. Leaf litter was more decomposed in the carp only ponds compared to controls, while there was no significant effect on cotton strip decomposition. Aquatic plants were absent in the Cu + Carp ponds caused by the combined effects of Cu toxicity, carp disturbance and the increase in turbidity due to bioturbation. Increases in periphyton cover in Low Cu + Carp, while absence in the High Cu + Carp ponds, and differences in the decomposition of surface and buried cotton strips were not as predicted, which highlights the need for such studies to understand the complex interactions among stressors.