Aim  Urbanization usually leads to biotic homogenization with a decrease in native species and increase in exotic species. We investigated whether local environmental factors in urban water bodies, such as water quality, habitat structure and biotic interactions, influenced the invasion of these systems by exotic macroinvertebrate species. Location  Urban surface water systems in lowlands of the Rhine‐Meuse delta. Methods  Presence and abundance of native and exotic macroinvertebrate species were compared between different urban water types and related to environmental variables with multivariate analysis and spearman’s correlations. Moreover, co‐existence of related native and exotic species was studied. Results  In total nine exotic species were found in the following taxa: Tricladida (1), Crustacea (5), Bivalvia (1) and Gastropoda (2). Taxonomically related native and exotic crustacean species did not seem to be influenced by competition in nutrient‐rich urban waters; most species showed high abundances. Nevertheless, two exotic crustacean species were much more abundant in waters where other crustacean species were absent, possibly filling empty niches. Native species richness and abundance was positively related to environmental heterogeneity in the form of submerged vegetation. The occurrence and abundance of most exotic species were positively related to several eutrophication indicators, such as nitrate, sludge layer and lemnid vegetation. Main conclusions  Exotic species in urban waters were mostly detritivorous or omnivorous and therefore dependent on leaf breakdown. In nutrient‐rich water systems, where food availability was high, exotic crustacean species co‐existed with native crustacean species, while in nutrient‐poor, richly vegetated systems, native Asellidae dominated exotic Asellidae. In the turbid water bodies with very little vegetation, native species richness was low and two exotic crustacean species were relatively abundant in these water systems. Invasibility of urban water systems could be reduced by stimulating the development of submerged and nymphaeid vegetation and decreasing nutrient levels.