The aim of this study was to determine the diversity of fish species, and the role of the Bogowonto River estuary as the nursery and feeding ground of fishes. Seven sampling stations were determined in the estuary of Bogowonto River. Fish samples were identified, and measured the length and weight. The results showed that 2235 fishes were caught consisting of 38 species. The monthly Shannon-Wiener diversity index (H’) ranged from 1.05 to 2.38, while the evenness index (E) ranged from 0.44 to 0.74, and the species richness index (D) ranged from 0.22 to 0.45. The diversity index at each station showed the range of 1.72 to 2.29, and the evenness index ranged from 0.59 to 0.85, while the evenness index ranged from 0.22 to 0.34. The presence of the most numerous species namely Mystus gulio had the occurrence of 35.35%, and the second largest number was Moolgarda engeli 14.08% then Ambassis macrachantus 11.54%. Most fishes were juvenile with average size of <10 cm and weight <15 g. Bogowonto River estuary has played an important role in providing a nursery, feeding and spawning ground for marine, brackish and freshwater fishes.