We analyzed the patterns variation of blue and green waters in the Yellow River Basin from 1998 to 2020 and evaluated the contributions of climate change and human activity on those variations. During the study period, both blue water volume and green waters flow increased overall across the Basin. Water withdrawal and water consumption showed an increasing trend, mainly due to increases in domestic and ecological water withdrawal and water consumption; the trend concentrated mainly in the Toudaoguai (TDG) area. Water return flow showed a decreasing trend, mainly due to decreases in agricultural and industrial water return flow in the Yellow River Basin. Throughout the study period, blue water volume and green waters flow were higher in the west than in the east, while precipitation was higher in the southeast than in the northwest. Changes in land cover were able to explain 87% of the observed variation in water return flow and 95% of the observed variation in water consumption. Changes in land cover indirectly affected blue water volume (the path coefficient β = 0.209) and green water flow (β = 0.273). Through its influence on precipitation, climate change affected blue water volume and green waters flows (β > 0.8). Through its influence on water consumption, water withdrawal affected green water flows (β = 0.4), the extent of which depended on precipitation. These findings highlight the need for efficient water management in the Yellow River Basin to ensure the long-term health of its ecosystems.