To evaluate the water quality in the Poprad, Kamienica, Dunajec river and the Łubinka stream in the Sącz agglomeration, two series of pilot studies were conducted on raw water samples, with a particular focus on both physical parameters (such as total suspended matter, turbidity, pH, and conductivity) and chemical parameters. The analysis presented increased concentrations of phosphorus, nitrogen, BOD5, COD, chlorides, sulfates, permanganate value, orthophosphates, total suspended matter, specific electrolytic conductivity (PEW), pH levels, and various elements including lithium, magnesium, manganese, potassium, sodium, calcium, and iron. No exceedance of the detection limits for individual pesticides were observed in the waters of the Poprad, Kamienica rivers and the Łubinka stream. Nevertheless, increased concentrations of the insecticide imidacloprid and the fungicide imazalil were detected in the Dunajec river. The primary factors impacting water quality in the Sącz agglomeration are the use of fertilizers, the proximity of wastewater treatment plants, and the presence of landfill sites.