Nepal has a high annual rainfall, but it still faces numerous challenges in ensuring good water quality. A total of 20 water samples were collected from five springs, seven rivers, one borehole, and seven reservoir tanks. pH, electrical conductivity, total dissolved solids, turbidity, total hardness as CaCO3, and residual chlorine in the water samples were all found to be within the National Drinking Quality Standards (NDWQS) and World Health Organization (WHO) recommendations. The chemical oxygen demand (COD) was calculated in the range of 35.65–70.826 mg/L, where most of the water samples exceeded the WHO's threshold. The mean biological oxygen demand (BOD) value was 2.929 mg/L, which was below the WHO tolerance level. Moreover, the concentrations of zinc, copper, chromium, arsenic, cadmium, lead, chloride, fluoride, nitrate, nitrite, sulfate, and phosphate species studied here were lower than those of the NDWQS and WHO standards. It was found that most of the water samples crossed the threshold standard for Escherichia coli and total coliforms, respectively. The iron concentrations in BW8, PW9, and RVW10 were estimated at 0.321, 0.301, and 0.367 mg/L, manganese in BW8, RVW10, and PW9 at 0.191, 0.142, and 0.104 mg/L, and selenium in RVW10 and RVW14 at 0.041 mg/L, which exceeded the WHO permissible limit. In most samples, the contamination factor (CF) values of COD exceeded unity, and the pollution load index (PLI) was calculated at 1.3. In the CF analysis of Fe, Mn, and Se, it was found that some water samples were polluted and not suitable for drinking. Statistical analysis of water quality parameters revealed a significant correlation. Overall, the results suggest that governments and development agencies should enhance their involvement in water resources management to ensure sustainability.