Background Stock enhancement of freshwater fisheries in large water bodies is a vital green development strategy in China.

Objective This study aims to clarify fish community structure, spatial-temporal distribution and stock abundance in Hongkou Reservoir, and provide scientific references for ecological fish enhancement.

Methods We conducted two surveys on the reservoir based on a combination of traditional catch surveys in February, May, August and November 2024 and hydroacoustic detection in August and December 2024.

Results A total of 21 species ,3 orders, 5 families and 18 genera were identified during the catch surveys.Coptodon zillii, Hypophthalmichthys nobilis and Sarotherodon galilaeus were dominant species, and Culter alburnus, Hemiculter leucisculus, Distoechodon tumirostris were important species. The results of hydroacoustic detection showed that fish populations were mainly small sized individuals with total body length of 1.2–7.0 cm (TS: −70.3 to −55 dB) and average length of 5.68 cm, accounting for 83.90% in summer and 47.59% in winter. The average fish density reached 8171.09 ind/hm² in summer and 2003.70 ind/hm² in winter, with estimated fish stocks of 583.09 t and 682.68 t respectively. Horizontally, high fish density occurred in the dam area in both seasons, and two tributaries at the reservoir tail area near Houlong River and Jinzao River are also the main gathering areas for fish in winter. Vertically, fish concentrated in 2–7 m water layer in summer, and migrated downward to 7–12 m layer in winter.

Conclusion Fish community in Hongkou Reservoir was jointly affected by invasive alien species and stocked enhancement fish, showing distinct spatial-temporal heterogeneity. The results provide fundamental support for alien species prevention, scientific stocking and sustainable fishing management in the reservoir.