Abstract: Ecosystem services play a crucial role in maintaining and influencing the water environment within a basin. Promoting positive synergies between ecosystem services and avoiding negative trade-offs are of significant importance for watershed water environment management and sustainable development. To address the significant water environment issues in the Nansi Lake Basin, and with the goal of achieving sustainable development of agricultural economy and water environment of the basin, the spatiotemporal characteristics of multiple ecosystem services (crop supply, livestock supply, aquatic supply, water yield, water purification, soil conservation) from 2005 to 2020 were quantitatively evaluated. The study utilized correlation analysis, Structural Equation Modeling, and Partial least squares regression to investigate the trade-off relationship between ecosystem services and identify the key drivers influencing water purification services in the watershed. Additionally, ecological function zoning of the watershed was conducted using the k-means spatial clustering method. The results revealed that: (1) The high-value areas of crop production were mainly distributed in the western plain area of the watershed, while the high-value areas of water yield and soil erosion, as well as the low-value areas of nutrient export were in the eastern hilly area of the watershed. (2) Trade-offs between crop supply service and water purification services were significant in the Nansihu Lake basin. (3) Sown crop area, total agricultural machinery power, and fertilizer application were the key drivers of water purification services in the watershed. (4) The watershed can be divided into three ecological function zones: the main agricultural production zone, the ecological conservation zone and the water quality safety zone, while the focus on agricultural development and ecological protection should be different in each zone. In view of the significant trade-offs between crop supply services and water purification in the Nansihu Lake Basin, it is urgent to strengthen the collaboration of stakeholder departments, integrate the main function zoning and ecological environment zoning control, and implement spatial planning for the sustainable development of the economy and the water environment. By optimizing and regulating the scale, structure, and mode of planting in each zoning area, we can reduce nitrogen export while improving the economic benefits of the basin, coordinate ecosystem service trade-offs, and provide decision-making support for the integrated management of the watershed’s water environment and sustainable development.