Salinization of freshwater ecosystems is a global problem affecting many regions worldwide and can co-occur with pesticides in agricultural regions. Given that both stressors are potent to affect macroinvertebrate communities, their effects could interact. We investigated the effects of salinity and pesticides at 24 sites in an agricultural region of southern Victoria, South-East Australia. We used distance-based redundancy analysis to determine the influence of pesticides, salinity and other environmental variables on the composition of macroinvertebrate communities. Salinity and pesticide toxicity had a statistically significant effect on communities as had the substrate composition and the percentage of pool and riffle sections in the sampled stream reaches. We did not find evidence for interactive effects between salinity and pesticides, i.e. the effect of one of these variables did not depend on the level of the other. Nevertheless, our results show that salinization and exposure to pesticides can be major factors for the structure of macroinvertebrate communities in agricultural regions. Pesticide toxicity acted on a lower taxonomic level compared to salinity, potentially indicating evolutionary adaptation to salinity stress.