The Pearl River estuary fishery is one of China's four renowned fishery waters and is also among the most human-impacted aquatic regions. To assess the effects of stock enhancement on the ecosystem and ecological capacity of estuarine waters, this study utilized historical and contemporary survey data on fishery resources and ecological envrionment. A 6-year material balance model of the Nanlang waters was constructed using Ecopath with Ecosim (ewe) 6.5 software to systematically analyze changes in ecosystem energy flow, general characteristics, and food web structure. The results indicated that in 2005 and 2016–2020, energy flow in Nanlang waters was primarily concentrated in trophic levels Ⅰ–Ⅳ, with a consistent nutritional structure. The grazing food chain and detritus food chains were the dominant energy pathways, characterized by high energy utilization rates among primary producers but low overall energy flow conversion efficiency. The ecosystem was in a development stage. Compared to 2005, fishery resources biomass, trophic levels, and system energy conversion efficiency increased from 2016 to 2020. The total primary production to respiration ratio (TPP/TR) of the system gradually approached 1, while the system connectivity index (CI) and system omnivory index (SOI) slightly rose, indicating a maturing ecosystem with an expanding overall scale. Additionally, the ecological capacity of Lateolabrax japonicus and Acanthopagrus latus increased by 5 and 94 times, respectively, in 2020 compared to 2005. In conclusion, stock enhancement not only enhances the stability, complexity, and maturity of the estuarine ecosystem but also significantly improves its ecological capacity.