Freshwater ecosystems and associated habitats harbor incredible biodiversity. They offer various ecosystem services and sustain human livelihoods. However, due to increasing developmental pressure and rising water demand, these systems are under huge threat. As a result, many aquatic species are feared to become extinct in near future. Quantifying the patterns of aquatic species diversity and composition of river systems is urgently required. With this interest, we studied four river systems in the Western Ghats region, documenting the pattern of fish diversity and identifying the factors that influence fish species richness. Maintaining undisturbed streams and river basins, especially headwater regions is crucial for sustaining freshwater biodiversity in the tropical river ecosystems.