Freshwater ecosystems in Kosovo have undergone significant degradation in recent years due to various anthropogenic pressures, including sewage effluents, industrial discharge, water intakes, and riverbed degradation. Consequently, the populations of freshwater biota, including bioindicators, have been heavily impacted by these activities. This study provides a thorough evaluation of water quality in the main course and tributaries of the Ibër Basin, Kosovo, utilizing macroinvertebrates and benthic diatoms as bioindicators. The well-being of aquatic ecosystems is intricately tied to water quality, and these organisms serve as valuable indicators because of their sensitivity to environmental changes. Sampling of macroinvertebrates and diatoms were collected at 20 stations in the basin. Diversity, abundance, and ecological indices obtained from macroinvertebrates and benthic diatoms were employed to assess the water quality status at various sampling sites. The findings indicate variations in macroinvertebrate and benthic diatom assemblages among different sites, reflecting anthropogenic impacts on water quality in most of the studies sites. The macrozoobenthos structure during this investigation consists of one class (Gastropoda), two subclasses (Hirudinea and Oligochaeta), nine orders (Diptera, Isopoda, Coleoptera, Hirudinida, Amphipoda, Decapoda, Trichoptera, Ephemeroptera, and Plecoptera), and 26 families. The composition of diatoms includes 152 species, with the most diverse genera being Nitzschia Hassall 1845 (29 species), Navicula Bory, 1822 (18 species), and Gomphonema Ehrenberg, 1832 (9 species). The integration of biological and environmental data provides a holistic understanding of the ecological health of freshwater ecosystems of the Ibër Basin indicating severe deterioration at several of the study sites. The outcomes of this study can inform water resource management strategies, facilitating targeted conservation and remediation efforts to improve and preserve the overall water quality in the basin. This research contributes to the broader field of freshwater ecology and underscores the significance of using bioindicators for effective water quality monitoring and management.