We studied faunistic and ecological factors influencing distributions of aquatic beetles in the Northern Western Ghats (NWG) of India. In the period 2013–2017, we collected 213 samples from 105 localities within the area and obtained 66 species, the majority of which belong to Dytiscidae. Relative occurrence based on incidence data revealed that dytiscid water beetle Laccophilus inefficiensas the most widespread species. Non-parametric richness estimators Chao2, Jackknife1 and Bootstrap showed that 70–80% of the fauna was covered in the sampling efforts from different types of freshwater habitats. Sample-based rarefaction suggested that more sampling efforts within the region can yield additional species. Canonical correspondence analysis (CCA) revealed that altitude, salinity, hydroperiod and depth influenced the distribution of aquatic beetles. Further, CCA also revealed habitat preference and co-occurrence of various aquatic beetle species. For instance, while co-occurring species under Laccophilinae and Hydroporinae were eurytopic, other co-occurring species Clypeodytes hemani, Microdytes sabitaeand Lacconectus lambaiwere restricted to temporary habitats. Multiple correspondence analysis (MCA) showed a strong association between altitudinal classes and species distribution where many species were restricted within a particular altitudinal gradient. For example, M. sabitae, C. hemani, Hygrotus nilghiricus, L. lambaiand Rhantus taprobanicuswith classes 900–1199 and 1200–1499 while Hyphydrus flavicans, Laccophilus ceylonicus, Lacconectus andrewesi, Sternolophus inconspicuusand Canthydrus laetabiliswith the class 300–599. The present work on aquatic beetles is the first attempt to study the influence of environmental factors on species diversity and distribution in the Northern Western Ghats of India.