Water flow regulation is an important ecosystem service that significantly impacts on ecological quality and social benefits. With the aim of improving our understanding of ecosystems and proposing strategies for optimizing ecosystem services, a geographic information system (GIS)-based approach was designed to estimate and map regulated water flow in the Chongqing region of China. In this study, we applied the integrated valuation of environmental services and tradeoffs (InVEST) model and mathematical simulations to estimate the provision of the regulated water flow across space and time in 2000, 2005, and 2010. The results indicated that this ecosystem service had improved by 2.07 % from 2000 to 2010 as a result of human activities (such as vegetation restoration) and climatic interaction. Places with positive changes mainly occurred in high mountain areas, whereas places with negative changes were mainly distributed in resettlement areas along the Yangtze River. The type of ecosystem in areas with high mountains and steep slopes was a relatively minor contributor to the total service, but this ecosystem had the higher water flow regulation capacity. Moreover, with the increase in altitude and slope, the percentage contribution of forest increased significantly from 2000 to 2010; by contrast, the percentage contribution of cropland decreased rapidly. As for the impacts, the spatial variation of water flow regulation in the Chongqing region had a significant relation with climate and human activities at the regional scale. These results provided specific information that could be used to strengthen necessary public awareness about the protection and restoration of ecosystems.