During the spring of 2011, forty-five macrozoobenthos samples were taken from streams and rivers all over the Dragash Municipality in order to assess the impact of inhabited areas in these freshwater ecosystems, considering the fact that there is no sewage treatment and waste management is dysfunctional in many parts of this Municipality. On the basis of the habitat structure evaluation, basic physical and chemical analysis and Family Biotic Index according to Hilsenhoff and EPT Index (Ephemeroptera Plecoptera Trichoptera), this study shows that the freshwater ecosystems in the Dragash Municipality are heavily polluted and impacted by human activities in their midstream and downstream segments. The main sources that deteriorate their natural ecological conditions in these segments are: load of all kinds of waste directly into the rivers and streams, industrial discharge into the freshwater ecosystems and the direct sewage discharge into the rivers and streams all over the municipality. This study also shows that the freshwater ecosystems of the area in their upper reaches are home to very interesting and rare composition of aquatic fauna. Several species and many potential ones which live only in this area and nowhere in Kosovo or abroad, or their distribution elsewhere is very limited, have been found.