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The conservation and management of inland fish and freshwater ecosystems immensely contribute to global sustainable development. The existing 'Protected Area' (PA) network does not represent freshwater resources well and seldom considers its fish communities, while designating PAs. A study was undertaken to quantitatively assess the role played by the three terrestrial PAs (IUCN category IV) in conserving fish diversity and preserving habitat quality in the river reaches bordering the three PAs of the river Pranhita. It is a unique river system in the Indian Deccan Plateau in terms of fish diversity and community structure. Field surveys were conducted during the non-monsoon and monsoon seasons in 2020–21, that recorded 53 species including endemic and threatened fishes from river Pranhita, which represent more than one-third the number of fish species of Telangana state. The higher diversity and lower dominance index value (p < 0.01) reported in PAs compared to Eco Sensitive Zones and unprotected areas during the non-monsoon season indicate the role of intact physical habitat in providing refuges to the fish species in monsoon dependent tropical rivers. The optimal water quality revealed no significant difference (p > 0.0001) between protected and unprotected river reaches, and healthy biotic integrity assessed on the basis of fish community structure was attributed to the contiguous flow and less anthropogenic disturbance. This study supports that it can be considered as a representative zone for the conservation and protection of indigenous and endemic fish species of the Godavari Basin. The results concluded that the scope of the terrestrial PA network in India could be potentially extended to their bordering aquatic ecosystems, especially rivers to maintain pristine habitat conditions and conserve the fish genetic resources to ensure the flow of ecosystem services. [ABSTRACT FROM AUTHOR]