It has not been well known how climate and habitat variables will influence the distribution of plant species to some extents at mesoscales. In this report, by using the distribution of aquatic plants in Western Ghats, a biodiversity hotspot in tropical Asian region, I quantify the relative importance of climate and habitat variables on structuring spatially species richness and taxonomic diversity patterns using structural equation modeling. All the sampling qudrats in the region used for the study has a spatial resolution of 0.5 latitude × 0.5 longitude. The results showed that species richness is high in both northern and southern part of the region, while low in the middle part. In contrast, taxonomic distinctiveness is relatively homogeneous over all the sampling quadrats in the region. Structural equation modeling suggested that taxonomic distinctiveness patterns of aquatic plants in the region follow temperature (partial regression coefficient=0.31, p<0.05) and elevational (partial regression coefficient=0.31, p<0.05) gradients, while richness patterns cannot be explained by any of the currently used variables. In conclusion, environmental variables that are related to taxonomic distinctiveness would not be related to richness, given the fact that these two quantities are orthogonal more or less. Both climate and habitat are equally influential on taxonomic distinctiveness patterns for aquatic plants in Western Ghats of India.