Globally, the river ecosystems are threatened due to human-driven exploitation and indiscriminate resource use. The rate of species loss is a magnitude higher in these ecosystems, hence, identifying conservation priority areas as refugia, using the flagship-cum-indicator species approach can aid in long-term conservation of multiple species and ensure uninterrupted functioning of ecological processes. For effective conservation planning, we derived the site occupancy and abundance of Gangetic dolphin (Platanista gangetica) as a flagship species in the Ganga River Basin, and modelled their distribution vis-à-vis river conditions for identifying Conservation Priority Stretches (CPS). The study incorporates the first-ever basin-wide (4635 km river) Gangetic dolphin (GD) sightings to estimate range decline, abundance, and identify CPS of select rivers in the Basin. A total of 2151 sightings of surfacing dolphins with mean encounter rate of 0.55 ± 0.09 sightings/km of the river was observed from the surveyed stretch. The GD encounter rate varied significantly across the surveyed rivers (Analysis of Variance, F = 3.08, p < 0.001). We estimated 24.37 % decline in the dolphin distribution range in the basin since 19th Century. The estimated population size of the dolphin in the Basin was 3330 individuals ± 620 individuals (Confidence Interval 95 % = 2304–4668; Coefficient of Variance = 18.61) which varied across the river. The site occupancy and abundance were best predicted by channel depth (β = 0.82 ± 0.46), meanders (β = 02.56 ± 0.87) and individual rivers, whereas channel width (β = 0.11 ± 0.08) and survey efforts influenced detection probabilities. Further, we identified 610 km (12.2 %) of river stretches as high CPS in the Basin based on the prediction probability (≥0.70) of GD. Protection of these stretches is likely to ensure sustained reproduction of GD and provide refugia for other threatened species of the Ganga River and its tributaries, which is under increasing anthropogenic pressure. © 2022 The Author(s)