The effect of urbanization is often reflected both in lotic and lentic habitats, through changes in diversity and structural and compositional changes in macroinvertebrate communities. In this study, we focused on macroinvertebrate assemblage in lotic and lentic ecosystems of the Krąpiel River catchment area (NW Poland) with the following aims: (1) to determine the main driver in structuring lotic and lentic macroinvertebrate communities and the factors that influence them in urban versus rural landscapes; (2) to test whether the diversity of macroinvertebrate assemblages in urban lotic/lentic ecosystems is lower than that in rural landscapes; (3) to identify characteristic macroinvertebrate species for urban and rural lotic/lentic ecosystems; to (4) determine species tolerance ranges and species optimums, with special emphasis on characteristic “urban” and “rural” species. Distance from study sites to built-up areas and conductivity were the main factors contributing to the separation of urban vs. rural habitats. For lotic sites, temperature, the percentage of built-up area, insolation, and oxygen concentration were the main factors significantly associated with changes in community composition. For lentic sites, insolation, temperature, and BOD5 were recognized as the main factors which are significantly associated with changes in community composition. The results for lentic habitats were as expected: average species richness was higher in rural than in urban habitats. The characteristic species for each of the four habitat groups included Mideopsis orbicularis for Lentic rural habitats; Hygrobates longipalpis for Lotic rural habitats; Piona sp. for Lentic urban habitats; Mideopsis crassipes for Lotic urban habitats. Hygrobates longipalpis and Piona sp. were at the opposite sides with respect to the degree of urbanization. Result of this investigation has shown that the impact of urbanization and consequently the implementation of conservation measures should be viewed separately within the lentic and lotic gradient.