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The aim of this study, conducted in accordance with both European Union and national legislation, was to evaluate the physicochemical conditions of the Rega River in northern Poland, where efforts are underway to restore its watershed for migratory fish. From 2018 to 2022, water temperature, dissolved oxygen (DO), pH, total suspended solids (TSS), conductivity, alkalinity, total hardness (TH), biochemical oxygen demand (BOD5), chemical oxygen demand (CODCr), nitrite nitrogen (NO2-N), ammonium nitrogen (NH4-N), and total phosphorus (TP) were measured at nine monitoring sites. The results showed that TSS and nitrite nitrogen (NO2-N) were the main factors threatening the suitability of the Rega River as a habitat for salmonid fishes. Additionally, maximum water temperatures occasionally exceeded the tolerance limits for these fishes. Seasonal variations in nitrogen and phosphorus forms, and the dependency of nitrogen forms on DO, indicated disruptions in natural biochemical processes due to surface runoff pollutants from the watershed. This includes fertilizer runoff from agricultural fields and municipal pollution from the towns through which the river flows. The findings underscore the need for continuous monitoring of Rega River waters to safeguard the habitat conditions required by environmentally sensitive fish species.