<p>Hydropower dams play a major role in changing the water quality of river ecosystems, making them one of the factors important to decision-making for sustainable hydropower development. We hypothesized that water quality changes with reduced flow in the dewater area due to hydropower dams in the Marsyangdi and Trisuli rivers of the Gandaki basin. Water quality variables were analyzed from five sampling sites, which included reference, disturbed, and recovery sites, during three seasons covering the post-monsoon (November), base-flow (late February), and pre-monsoon (April) periods during 2021 and 2022. As 60 water samples were collected from the two rivers in each season, with six replicates collected from each station, the total number of samples was 180. Fourteen physicochemical parameters were analyzed: pH, temperature, chloride, electrical conductivity, turbidity, dissolved oxygen, total dissolved solids, alkalinity, free carbon dioxide, calcium and total hardness, nitrate, phosphate, and ammonia. The results revealed that the hydro project dams had an effect on the physicochemical parameters. Most importantly, the site where water was abstracted (the dewater area downstream of the weir) was the most impacted in terms of temperature and dissolved oxygen, which may have effects on aquatic life in both rivers. Higher turbidity and phosphate concentrations also suggest more contamination by pollutants in both rivers. In summary, the diversion hydropower dams impacted the dewater zone, particularly during the base-flow season. The results of this study call for sustainable hydropower developments to maintain mandatory flow release downstream of dams, particularly during the base-flow season.</p>