Abstract: As a type of water source with special supply requirements, maintaining the water ecology of lake–reservoir type water sources in a healthy state is an important prerequisite for achieving drinking water safety. As an adaptive strategy of human adjustment to the natural environment, water diversion projects have long been a focus of research, both domestically and internationally, regarding their impact on the ecological environment of receiving water bodies such as lakes and reservoirs. To examine the characteristics of the hydro-ecological environment of lake–reservoir type water source areas under extreme drought conditions and the influence of water transfer projects, Shahe Reservoir, a typical lake–reservoir water source in the western hilly and mountainous area of the Taihu Lake Basin, was taken as an example. The response characteristics of water quality and aquatic ecology to drought and water transfer input were explored using statistical methods and mechanistic models. The Shahe Reservoir is located in a representative lake–reservoir water source basin upstream of the Taihu Lake Basin, where water quality and aquatic ecology have been monitored for a long time and have also drawn the attention of many researchers. Results showed that severe drought from 2022 to 2023 significantly lowered water levels,impacting transparency and total nitrogen (TN) level. The reservoir has basically reached a state of moderate to mild eutrophication, with chlorophyll-a, water temperature, permanganate index, and total phosphorus exerting the greatest influence on algal density. There are marked spatiotemporal differences in the distribution of algal communities in Shahe Reservoir, and the correlations between different algae and specific environmental factors vary considerably. The composition of benthic animal communities is dominated year-round by insect biomass, with the dominant species differing across monitoring sites. The total abundance of benthic organisms is positively correlated with physical parameters and light conditions, whereas benthic biodiversity is positively correlated with nutrient load. The permanganate index and total nitrogen concentration of the reservoir increased in the short term before and after the recent water supplementation project but gradually stabilized. Based on the PCLake+ model simulations, it was shown that under the influence of different types of water quality inputs, chlorophyll-a responds more slowly to external disturbances compared with total nitrogen and total phosphorus, and this effect gradually weakens with the end of water replenishment and the reservoir’s self-regulation. Drought conditions exert a pronounced impact on the aquatic ecological environment of lakes and reservoirs, manifested in shifts in key water quality indicators, algal dynamics, and benthic community structure. Under this background, water regulation and input, serving as an important approach to mitigating drought, require careful consideration of their long-term effects, including changes in scale, timing, and other factors, on the functions of lakes and reservoirs. The response speed and self-regulating mechanisms of the aquatic ecological environment in reservoirs to the quality of regulated and transferred water are also critical issues that need to be studied in the future. By combining statistical analysis and mechanistic models, this study analyzes the impact mechanisms of drought conditions and water diversion practices on the aquatic ecological environment of lake-reservoir type water sources from past, present, and future perspectives. This provides a theoretical foundation for the rational development and utilization of reservoir-based water sources, ensuring drinking water safety in urban and rural areas, and scientifically protecting the aquatic ecological environment under climate change. With the vigorous advancement of national water network construction, an increasing number of lake-reservoir type water sources will be affected by water diversion and input. Therefore, it is urgent to strengthen research on the impacts of such interventions on the water quality and aquatic ecology of receiving water bodies.