Small urban water bodies serve multiple functions within urban ecosystems. However, they often experience significant external pollution and possess limited self-purification capability. The Dishui Lake in Shanghai is a typical urban lentic system, and encounters various ecological challenges. Since 2007, the local authorities have implemented a systematic biomanipulation program, aiming at improving the water quality by enhancing the stock of filter-feeding fish like silver carp (Hypophthalmichthys molitrix) and bighead carp (Aristichys nobilis). Yet, due to the lack of understanding on some key scientific issues such as the current state of the ecosystem, ecological carrying capacity, and the optimization of stock enhancement strategies, the effect of the stock enhancement has not been satisfactory. This study encompasses three primary research components: (1) a quantitative analysis of the current ecosystem structure; (2) a quantitative assessment of the ecological carrying capacity of silver carp and bighead carp; and (3) a prediction of the effects of different strategies on the ecosystem. Related findings are expected to provide a significant foundation for the optimization of stocking strategies in the Dishui Lake, as well as similar urban water bodies. This study was conducted utilizing the Ecopath with Ecosim (EwE) model, which is adept at simultaneously simulating both the static characteristics (Ecopath) and the dynamic processes (Ecosim) of the ecosystem. Primary data for the model were obtained from ecological surveys conducted in the Dishui Lake during 2023 to 2024, while model parameters that were challenging to measure directly were supplemented with reference data from analogous lakes. Importantly, stable isotope analysis was employed to refine the food matrix. Subsequently, an Ecopath model including 15 functional groups was developed for the Dishui Lake to evaluate the status of the ecosystem along with the ecological carrying capacity of silver carp and bighead carp. Ecosim was employed to simulate the potential ecological impacts of various biomanipulation scenarios within the ecosystem. The findings indicated that trophic levels of the 15 functional groups varied between 1.00 and 3.50, while the ecotrophic efficiency ranged from 0.12 to 0.98. The total system throughput for the Dishui Lake was calculated at 3376.93 t/(km² ·a), with a ratio of total primary production to total respiration of 1.59. The connectance index (0.29) and the system omnivory index (0.09) suggested that the ecosystem is at an immature developmental stage. Trophic levels derived from stable isotope analysis exhibited strong correlations with those estimated from Ecopath (R² =0.88, P＜0.01), validating the reliability of the food matrix. The ecological carrying capacity of silver carp and bighead carp was estimated at 22.01 t/km², which was approximately 1.33 times the current biomass. The Ecosim simulation results indicated that increase in the fishing mortality of silver carp and bighead carp would indirectly reduce the biomass of top predators. When the biomass of silver carp and bighead carp reached their ecological carrying capacity, it significantly impacted phytoplankton and zooplankton communities. The current predominance of bighead carp over silver carp was found to be suboptimal for effective algal control. Notwithstanding limitations including parameter uncertainty and unaccounted predator diet plasticity, this study suggests: a gradual increase in the biomass of silver carp and bighead carp; the optimization of the stocking ratios between silver carp and bighead carp; the implementation of integrated management strategies which combine controlled harvesting with multi-trophic stock enhancement; and the establishment of adaptive monitoring protocols. These findings provide a scientific foundation for optimizing biomanipulation strategies in the Dishui Lake and similar urban lentic systems.