Ephemeral rock pools are a characteristic type of aquatic habitat formed on the rock outcrops throughout the world, which harbor unique flora and fauna. Due to their structural simplicity and small size, rocky pools form a unique model ecosystem for studying how local environmental parameters shape aquatic vegetation. We studied the species-environment associations between the aquatic flora of the rock pools from the Western Ghats of India to understand whether species occurrence is influenced by the environmental parameters and whether we can predict the species occurrence using environmental variables. Sixty-one rock pools from 26 rock outcrops occupying different altitudinal gradients of the northern Western Ghats were sampled along with their physical properties and chemical characteristics. Canonical correspondence analysis suggested that altitude, latitude, magnesium, sulphate influenced species occurrence in rock pools. Replacement of species belonging to genus Eriocaulon across the altitudinal gradient was observed. Analysis of Covariance showed that most of the species are influenced by altitude while for few species both altitude and baserock were important. Application of various supervised learning procedures suggested that Random Forest was the most efficient method to predict species occurrence based on environmental parameters of rock pools. Decision trees based on Random Forest classification showed that multiple environmental factors including physical and chemical parameters of rock pools simultaneously influenced the species occurrence in the rock pools of the Western Ghats. © 2022 E. Schweizerbart’sche Verlagsbuchhandlung, Stuttgart, Germany.