Two hydroelectric projects are operational in the upper and lower stretches of the river Alaknanda near Lambagarh and Srinagar that are respectively ~ 140 km apart. The health of the river ecosystem in the owing stretches between and below these projects was bio-assessed, based on widely used diatom indices and van Dam ecologic values computed by OMNIDIA software. Samples were collected from Birahi, the semi-natural stretch -53 km downstream of power-house, Narkota, the impacted stretch 27 km upstream Srinagar dam and Bagwan, the highly regulated stretch 22 km downstream Srinagar. IPS and IBD revealed mild pollution in upper and lower stretch compared to relatively elevate at Narkota. However TDI indicates moderate organic pollution at Birahi and Narkota, whereas the IDSE indicates low degradation at all stations. The prevalence of tolerant N-autotroph, β-mesosprobe, mesotrophic and aquatic to aerophilic categories of van Dam environmental variables indicate that a certain level of impact already persists due to organic-cum-nutrient load and perturbed ow-regime. The prevalence of eutrophic and moderate O2 categories shows that the ecosystem is in critical state at Narkota, causing a disrupted continuum.