This study evaluates the water quality of the Klina River in Kosovo in relation to urban discharges and other anthropogenic pollution sources. Water samples were collected from eight monitoring sites during summer and autumn 2025. The analysis included pH, dissolved oxygen (DO), BOD5, COD, NH4-N, NO3, total nitrogen (TN), PO4-P, total phosphorus (TP), and the heavy metals Fe, Cu, Mn, Cd, Zn, Pb, Cr and Ni. Results were compared with the ecological-status criteria of Administrative Instruction MESP-AI 16/2017 and with reference values for heavy metals. The analytical framework additionally included paired Wilcoxon tests with false-discovery-rate adjustment, Pearson correlation analysis, an adapted Water Quality Index (WQI), Heavy Metal Pollution Index (HPI), Metal Index (MI), contamination factors (CF), a reference-based Pollution Load Index (PLIref), and exploratory principal component analysis (PCA) and hierarchical cluster analysis (HCA). The results show a clear deterioration in water quality in sections influenced by urban and agricultural pressures. The most critical conditions occurred in the Skenderaj urban-influenced section, especially at M3 and M4, where DO reached extremely low values and BOD5, COD and nutrient concentrations indicated substantial organic and nutrient pollution. Cd, Mn and Fe exceeded reference values at several sites, while Ni exceeded the reference value only at selected downstream sites during summer. The paired analysis showed significantly higher DO and significantly lower pH, BOD5, COD, NH4-N, NO3, PO4-P and TP in autumn. M3 had the highest adapted WQI in both campaigns, and Cd was the most persistent metal concern. PCA and HCA consistently distinguished M1 as the least-affected station and M3–M4 as the principal monitored pollution hotspots. Using the lowest-category approach for the assessed physicochemical quality elements, M1 showed moderate conditions, whereas each of M2–M8 had at least one result below the displayed moderate range; this does not constitute a complete ecological-status classification. The findings support improved wastewater treatment, stricter control of untreated discharges and continuous seasonal monitoring before the river joins the White Drin River. Because the dataset comprises only two seasonal campaigns and no independent field replicates, the findings characterize the monitored 2025 conditions rather than a complete annual assessment or definitive source attribution.