The aim of this paper is to make a comparative analysis of benthic macroinvertebrate compositions in streams and rivers in Croatia with relation to different physical-chemical factors, especially nutrients. Samples were collected according to the AQEM method. At all the sites, 20 taxa were recorded of which Turbellaria, Gastropoda, Bivalvia, Oligochaeta, Hirudinea, Crustacea, Ephemeroptera, Odonata, Plecoptera, Heteroptera, Trichoptera, Coleoptera and Diptera were included in the present study. Water temperature mostly affected the composition of benthic macroinvertebrates to which it was inversely proportional. Nutrient enrichment, i.e., higher concentrations of ammonium, nitrates, nitrites, total nitrogen, orthophosphates and total phosphorus mostly affected Ephemeroptera, Plecoptera, Trichoptera and Diptera, by decreasing their diversity.