Land-use change alters the dynamics of freshwater ecosystem services flows by affecting both service supply (by influencing hydrological processes and runoff) and demand (via changes in human water use). However, few studies have considered the wide range of effects of land-use change on freshwater ecosystem services' flows. In this study, we distinguished the impacts of changing water supply and demand in the Aojiang River watershed, Fujian Province, China, an important water resource for more than seven million people. Rapid urbanization between 1991 and 2015 led to a minor increase of 2.5% in the supply of freshwater ecosystem services. However, demand increased by 96.3%, leading to a 25.7% overall decrease in freshwater ecosystem services flows. Downstream demand for freshwater increased substantially due to large shifts in agricultural, urban, and industrial activities. Our analysis provides detailed information on freshwater ecosystem services flows from supply to beneficiaries within a watershed, thus facilitating integrated watershed management and decision making. This study demonstrates how land-use change and ecosystem services' flows can be integrated both at local and regional scales for land-use management, water reallocation, and ecological compensation, thus promoting the sustainability of freshwater ecosystems.