Change in river basins due to the natural flow alteration is largely attributable to hydropower dam operations worldwide. The amount, duration, and degree of flow change brought about by Nepal’s recent explosion in hydropower production in Marsyangdi and Trisuli Rivers which are near to load centers of Nepal, have seen severe impact on these river ecosystems. The present study attempts to calculate hydrological alteration in the Marsyangdi and Trisuli Rivers near Kaligandaki Basin using Indicators of Hydrological Alteration (IHA) model. Thirty-three ecological parameters were assessed using range of variability approach to determine how electric dams affect rivers downstream. This study compared flow data from hydrological stations of two rivers spanning more than 20 years period, taking into consideration of pre- and post- dam impact periods into account, with a focus on hydrological alteration caused by dam influence. With HA values of 35.41 and 35.55, past a hydropower construction, the results demonstrate the mild influences of the dam in Marsyangdi and Trisuli Rivers, respectively. Of the 33 parameters analyzed, two and seven parameters have altered highly in Marsyangdi and Trisuli River, respectively. The hydrological modifications caused by dams on both rivers may have detrimental effects on aquatic ecosystems. The study’s findings may help Nepal’s hydropower policy makers, who are finding it difficult to comprehend the dynamic effects of dams on rivers.