This study assessed the seasonal variability of physicochemical conditions and selected organic pollutants in the Sitnica River, Kosovo, under contrasting hydrological conditions. Surface water samples were collected from 15 monitoring stations during a high-flow campaign in February/March 2023 and a low-flow campaign in September 2023. The investigated pollutants included organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), BTEX compounds, and chlorobenzenes. Physicochemical parameters indicated stronger anthropogenic pressure during the low-flow period, with increased organic load, nutrients, ionic content, and suspended solids. Organic pollutants were detected during both campaigns, but their seasonal behavior differed among contaminant groups. Total PCB concentrations were significantly higher during the high-flow campaign (p = 0.004), suggesting hydrological mobilization or resuspension of particle-associated residues. In contrast, total BTEX concentrations were significantly higher during the low-flow campaign (p = 0.005), indicating stronger recent local inputs under reduced dilution conditions. OCPs, PAHs, and chlorobenzenes showed pronounced spatial variability, with localized peaks rather than uniform seasonal trends. Screening-level comparison with European environmental quality standards indicated that selected legacy pesticides, PAHs, benzene, pentachlorobenzene, hexachlorobenzene, and trichlorobenzenes reached concentrations of potential environmental concern at specific stations. These findings confirm the coexistence of legacy and recent contamination signals in the Sitnica River and demonstrate that hydrological conditions influence pollutant transport, redistribution, and detectability. The study provides baseline information for seasonal monitoring, source identification, and risk-oriented management of organic pollution in the Kosovo Plain.