Climate variation will affect hydrological cycle, as well as the availability of water resources. In spite of large progresses have been made in the dynamics of hydrological cycle variables, the dynamics and drivers of blue water flow, green water flow and total flow (three flows), as well as the proportion of green water (GWC), in the past and future at county scale, were scarcely investigated. In this study, taking the Heihe River basin in China as an example, we investigated the dynamics of green and blue water flows and their controlling factors during 1980–2009 using five statistical approaches and the Soil and Water Assessment Tool (SWAT). We found that there were large variations in the dynamics of green and blue water flows during 1980–2009 at the county scale. Three flows in all counties showed an increasing trend except Jiayuguan and Jianta county. The GWC showed a downward trend in the Qilian, Suzhou, Shandan, Linze and Gaotai counties, but an upward trend in the Mingle, Sunan, Jinta, Jiayuguan, Ganzhou and Ejilaqi counties. In all the counties, the three flows and GWC had strong persistent trends in the future, which are mainly ascribed to rainfall variation. In the Qilian and Shandan counties, rainfall was the major controlling factor for the three flows and GWC. Rainfall controlled the green water and total flows in the Mingle, Linze and Gaotai counties; green water flow and GWC in the Suzhou county; green water flow, total flow and GWC in the Jinta and Ejilaqi counties. Our results also showed that the "Heihe River basin allocation project" had significant influences on the abrupt changes of the flows above-mentioned. Our results illustrate the status of the water resources at county scale, providing a reference for water resources management of inland river basins.