Amphibians show a high amount of species richness and endemism. Such diversity can be attributed to their microenvironment as amphibians display fine‐scale heterogeneity depending on the microhabitats they inhabit. Tadpoles are considered as good indicators for understanding microhabitat–species association as they reflect the breeding sites and signify species survival potential. In this study, we assessed the microhabitat factors influencing the distribution of tadpoles of three endemic frogs of the genus Nyctibatrachus namely N. jog , N. kempholeyensis , and N . kumbara from central Western Ghats, India. Forty‐three streams were sampled from three river basins, and stream characteristics were analyzed using generalized linear models. The results indicate that the tadpoles show specific microhabitat preferences and spatial niche partitioning. Among microhabitat variables, the slope significantly influenced the distribution of tadpoles of N . jog and N . kempholeyensis . The tadpoles of N . jog preferred steep slopes, while N . kempholeyensis tadpoles were found in gradual slopes with low water depth. For N. kumbara tadpoles, water temperature significantly influenced their distribution in the streams. Such spatial heterogeneity promotes the coexistence of these species supporting the niche theory. The study advances the understanding of how amphibian diversity from the Western Ghats is shaped at the microhabitat scale. The perennial streams that the Nyctibatrachus tadpoles inhabit are at risk due to anthropogenic activities. The findings of this study provide important baseline data that could be useful for the conservation of the endemic anurans in the Western Ghats, India.