Effects of anthropogenic and environmental stressors on freshwater communities can propagate to ecosystem functions and may in turn impede ecosystem services. We investigated potential shifts in ecosystem functions that provide energy for freshwater ecosystems due to pesticides and salinity in 24 sites in streams of southeast Australia. First, effects on allochthonous organic matter (AOM) breakdown using three different substrates (leaves, cotton strips, wood sticks) in coarse and fine bags were investigated. Second, we examined effects on stream metabolism that delivers information on the ecosystem functions of gross primary production and ecosystem respiration. We found up to a fourfold reduction in AOM breakdown due to exposure to pesticides and salinity, where both stressors contributed approximately equally to the reduction. The effect was additive as, no interaction or correlation between the two stressors was found. Leaf breakdown responded strongly and exclusively to exposure to pesticides and salinity, whereas cotton strip breakdown was less sensitive and responded also to other stressors such as nutrients. No functional redundancy for the effects of pesticides and salinity on leaf breakdown was observed. For wood stick breakdown, no relationship to environmental gradients was found, however, the sample size was lower. We did not detect effects of pesticides or salinity on gross primary production or ecosystem respiration. A reduction in AOM breakdown by pesticides and salinity may impair the ecosystem services of food provision and possibly water purification. Hence, future studies should examine the spatial extent of these effects.