The fish diversity of different estuarine habitats of the Gowthami-Godavari River was studied from 2014 to 2017. We recorded 231 species of finfishes belonging to 27 orders, 81 families, and 167 genera. Perciformes was the most speciose order, followed by Carangiformes and Clupeiformes. Of the 231 species, one is an Endangered species (Silonia childreni), three are Vulnerable (Tenualosa toli, Cirrhinus cirrhosis, and Wallago attu), three are Near Threatened, and 11 are Data Deficient species. We also recorded five exotic species from the study area, of which Oreochromis mossambicus was the most dominant. The major threats, including potential impacts of river regulation and climate change on the estuarine habitats of Gowthami-Godavari, are also discussed.