Although their effectiveness has drawn some attention, the unique impact of ecological conservation programs on hydrology and the comparative relationship between these effects and those of climate change remain unclear. We developed a method to quantitatively evaluate the hydrological effect of ecological conservation programs by combining a hydrological model and mathematical method and assessed the hydrological changes attributed to ecological conservation programs (2005-2015) in the source region of the Yangtze River in China. Through improved water retention capacity, ecological conservation programs induce annual streamflow decreased by 57% and the summer flood decreased by 78%, decreasing these streamflow amounts by 60.71 m(3)center dot s(-1) and 160.14 m(3)center dot s(-1), respectively. The ecological conservation programs decreased the streamflow concentration degree in the summer-flood season, indicating reduced river flood risk. However, climate change increased annual streamflow by 167.44 m(3)center dot s(-1), which offset a large part of the decreased annual streamflow caused by the ecological conservation programs. Streamflow and streamflow concentration degree in the summer flood season increased by 366.16 m(3)center dot s(-1) and 0.27, respectively, resulting in a final increase of 206.02 m(3)center dot s(-1) in annual streamflow in the summer-flood season and an increased flood risk, offsetting some of the positive effects of ecological conservation programs. The ecological conservation programs generally exhibited beneficial hydrological effects; however, these improvements were largely nullified by the negative effects of climate change.