Artificial emergency water source lakes have been built in most cities in the middle and lower reaches of the Yangtze River, China, to ensure water safety for residents. However, these new ecosystems are prone to algal blooms or other degraded water quality conditions. A newly built water supply lake in the lower reaches of the Yangtze River was selected as a model system to test whether the coordinated manipulation of fish and submerged macrophyte communities could enhance ecosystem function and quality. The coordinated manipulations spanned a five-year period, aiming to enhance both top-down and bottom-up control of phytoplankton. As a result of these manipulations, the catch per unit effort of small-bodied zooplanktivorous fishes decreased by >95 % from year two and remained low. The coverage and biomass of submerged macrophytes increased year by year. Water transparency increased from 1.07 to 3.33 m. Total phosphorus and total nitrogen showed a decreasing trend (not significant though). The annual mean biomass of Cyanophyta, Chlorophyta and Bacillariophyta decreased from 2.99 to 0.03 mg/L, 3.90 to 0.16 mg/L, and 3.50 to 0.3 mg/L, respectively. The biomass of phytoplankton in different groups decreased in all four seasons. The annual mean biomass of Cladocera and Copepoda remained low. The biomass of Cladocera and Copepoda decreased in summer, fall, and winter. The Ecosystem Health Index - increased from 15.9 to 32.0. The pros and cons of the various top-down and bottom-up control measures employed are discussed. This research presents a valuable case study on the enhancement of ecosystem structure and function in newly constructed emergency water supply lakes and offers insights into the restoration of other subtropical shallow lakes.