Corridors of Riverine habitat are crucial in conserving the genetic integrity of the endangered aquatic fauna, but their performance has been inadequately measured in numerous fragmented freshwater systems. This is an assessment of the effects of natural and manipulated river corridors on dispersal, gene flow, and population viability of threatened aquatic species in the long term. By combining population genomics with the characterization of the habitats on a large scale, we compiled a SNP and microsatellite database of several taxa that represented various degrees of mobility throughout the river network. Population genetic studies demonstrated that there was a high level of variation in allelic richness and inbreeding coefficients, with low-mobility species exhibiting high levels of F 5 (>0.10) and high mate pair F 8 (0.35), which implies strong genetic isolation. Mantel tests identified that there was significant Isolation by Distance (IBD) among species (R = 0.38 -0.74, p < 0.01), whereas Multiple Regression on Distance Matrices (MRDM) demonstrated that Isolation by Resistance (IBR) models with Effective Resistance better explained genetic differentiation, providing an increase of 7-17 percent in model fit. It is noteworthy that undisturbed riparian corridors and tributary linkages were correlated with less effective resistance, increased gene flow, and increased allelic diversity. The most pronounced responses to hydrological barriers were seen in species with limited mobility, which highlights their susceptibility to hydrological barriers. Corridors that were incorporated in changed landscapes by humans provided significance to connectivity even when both the integrity and condition of flow were maintained steady. The results of the study demonstrate the necessity to maintain functional riverine pathways, rehabilitate damaged channel segments, and include quantitative metrics of connectivity in conservation planning. Increasing the integrity of corridors is necessary to protect not only the evolutionary potential, but also to prevent greater resilience to future environmental change. This research paper proves that genetic tools coupled with spatial resistance modelling are an efficient framework to be used to assess and optimize conservation responses in endangered aquatic species.