The present study was carried out in three distinct biogeographic provinces of India: the Himalaya, the Northeastern region, and the Deccan Plateau. The investigations aimed to understanding the association between physicochemical characteristics of water bodies and their influence on diatom assemblages. The majority of water quality parameters and diatom assemblages exhibited significant variations across the biogeographic regions. Canonical Correspondence Analysis (CCA) revealed that water quality parameters, including turbidity, iron, and potassium, significantly influenced diatom assemblages at the local scale (within rivers). Generalized Linear Model (GLM) analysis revealed that water temperature significantly impacted the abundance of diatom communities in the Himalayas and the Northeastern region, whereas dissolved oxygen influenced diatom abundance in the Deccan Plateau. The ecoregional differences in climatic and geological features influenced overall water quality, which, in turn affected the diatom communities at regional scales. A total of 21 common taxa were recorded across all biogeographic provinces. Among these taxa, Ulnaria ulna, Achnanthidium affine, Achnanthidium lineare, Cocconeis placentula var. euglypta, Fragilaria pinnata, Navicula radiosa, Cymbella affinis, and Gomphonema olivaceum indicated their broad tolerance to environmental variables, which was confirmed by their abundance and frequency distribution. The Himalayan waters were more conducive to inhabiting Achnanthes, Navicula, and Cymbella species, while the Deccan Plateau supported a relatively higher diversity of Nitzschia spp. Our study suggests that diatom assemblages and abundance respond not only to water quality but also to overall ecoregional differences.