Environmental and anthropogenic factors are known to drive fish community structure in aquatic systems across the world. This study investigates fish assemblages in lower order streams across contrasting landscapes in central and eastern India. We documented the species diversity of these monsoon driven lower order streams in the two regions. We also investigated the potential common environmental drivers of richness and diversity and effect of season in these tropical streams. The study was based on seasonal data on abundance of fishes and environmental parameters collected between 2015–2017 from streams in states of Madhya Pradesh and West Bengal. Species diversity were compared across regions and seasons, based on their richness (SR) as well as diversity (Shannon index H'). Drivers of overall richness and diversity were analyzed using multiple linear regression methods, based on best subset selection. Analysis of data revealed high diversity in these streams in both regions. Cyprinidae, Bagridae and Channidae were the most dominant families in both regions. Despite the geographical and local ecological differences across the regions, common environmental parameters were found to influence richness and diversity across the two regions, indicating these as being key drivers of fish community structure. Water flow was a common factor driving both richness and diversity across both regions. Our study revealed a lack of seasonal effect in structuring fish communities in tropical streams. With stream and river ecosystems facing increasing threats due to habitat alterations and water quality degradation in countries such as India, a clear understanding of regional and local drivers of community structure of aquatic fauna is crucial. These results on the role of common environmental factors across ecoregions provides baseline information for understanding their ecological roles and developing management plans for important river basins and fish conservation in future.