Tropical freshwater ecosystems are severely threatened, endangering evolutionarily distinct and globally endangered species the most. Understanding the habitat preferences of these vulnerable species is crucial for effective conservation. This study investigated the habitat associations of Micrixalus kottigeharensis, an evolutionarily distinct and globally endangered frog, within a mixed-use landscape in the Western Ghats biodiversity hotspot. We surveyed 204 stream segments across 2500 hectares, recording species count and habitat variables, and analysed these relationships using a Generalised linear mixed modelling framework. Our findings show that M. kottigeharensis has a strong preference for specific microhabitats. They preferred streams with a greater percentage of emergent substrate, dense canopy cover and optimal water discharge---emphasising the importance of structurally complex habitats with healthy riparian vegetation. Conversely, ambient air temperature showed a negative relationship with species count, indicating potential sensitivity to thermal stress. The species preferred riffles over runs, pools, step-pools, and braided channels. Landscape-scale factors, such as land-use, also likely influence their distribution. Furthermore, their peak activity was observed during the post-monsoon season. These results highlight the critical role of specific microhabitats in determining the distribution of M. kottigeharensis. Additionally, they provide valuable insights, especially for landowners and managers of agroforests, for targeted habitat management and restoration strategies such as maintaining the natural stream flow, prevention of stream channelisation and mining, and nurturing riparian buffers, aimed at conserving this endangered species.