Referring to the Mekong River, it is the largest river in Southeast Asia’s Indo-Burma biodiversity hotspot, and it sustains a diverse range of fish species. In order to manage the river’s fisheries in a sustainable way, it is important to have a comprehensive understanding of population dynamics. This study focuses on the spotted catfish, Arius maculatus (Thunberg, 1792), which is commercially valuable and found in the estuarine areas of the Mekong Delta, Vietnam. Monthly samplings were conducted at Tran De and Dinh An estuaries from July 2017 to May 2019, revealing distinct patterns in the gonad-somatic index (GSI) and hepato-somatic index (HSI). The spotted catfish were found to breed throughout the year, with peak breeding periods in March and August. The length at first maturity (Lm) was determined to be 12.80 cm for males and 11.79 cm for females. The fecundity, although relatively low, was measured at 16 ± 3 yolks per female and 144 ± 60 hyalines. The Von Bertalanffy growth parameters were calculated as L∞ (the asymptotic length) = 20.6 cm, K (growth coefficient) = 0.5 year−1 , and t0 (theoretical age at zero length) = − 0.603 year− 1 . The length at first capture (Lc) was found to be 8.93 cm. Evaluation of the mortality rates revealed that the spotted catfish population is being overexploited, as indicated by an exploitation rate (E) of 0.695, which exceeds the optimum level of 0.50. It is crucial to implement effective management strategies to ensure the sustainable fisheries of Arius maculatus in the Mekong Delta estuary in Vietnam.