This research evaluated the water quality of the Prizren River using macroinvertebrates as bioindicators, given their sensitivity to environmental changes and their utility in assessing aquatic ecosystem health. Sampling was conducted at six sites (L1-L6) along the main course of the river and two macroinvertebrate-based ecological indices were employed to determine the water quality status: the Family Biotic Index (FBI) and the richness of taxa of orders Ephemeroptera, Plecoptera and Trichoptera (EPT). We identified macroinvertebrate taxa of 28 families (22 taxa of class Insecta and six – belonging to other macroinvertebrate groups). The values of the indices across the six sampling stations ranged between 1.3 and 9.2 for EPT family richness and between 3.4 and 6.6 for FBI. According to the data concerning macroinvertebrates, the water of the Prizren River was, overall, of good quality. There was severe water quality degradation at two downstream locations, emphasizing the necessity for enhanced water resource management. The findings indicated that the diversity and abundance of macroinvertebrates varied across different sites, reflecting the ecological health of the river and, indirectly, the impacts of human activities on water quality. This research provided insights into the ecological health of the Prizren River, offering а valuable basis for future conservation and remediation efforts.