The blue and green water are two key components of the freshwater cycle, reflecting the availability of water resources for human and ecosystems. Utilizing this concept to quantitatively assess water security is an appropriate method for effective regional water resource management. However, most current research tends to focus on human-consumed water resources neglecting to simultaneously reveal the spatial patterns and potential connections between blue and green water resources. The middle reaches of the Heihe River, located in the inland arid area of Northwest China, face intensifying conflicts between ecological conservation and socio-economic development. These conflicts contribute to a growing tension in water supply and demand, ultimately impacting region's sustainable development trajectory. By integrating geographical datasets from multiple sources, our study concentrates on the middle reaches of the Heihe River Basin, aiming to fill the gap by quantifying the availability of the blue and green water resources at the sub-basin level from 2000 to 2020. Subsequently, we incorporate water demand data to comprehensively assess spatial distribution and temporal changes in blue water security and green water security. The findings of our study indicate that (1) The reliability of our assessment is supported by high consistency between observed and simulated runoff during both the calibration and validation periods, with R² and NSE values exceeding 0.7. This underscores the robustness of our approach in evaluating blue and green water security. (2) Green water resources emerge as the primary water source in the region, with an annual average four times greater than that of blue water resources. Spatially, blue water resources is predominantly concentrated in the southern grasslands and agricultural areas along the main river channel. Green water exhibits a decreasing trend from the south to north. Despite these spatial differences, relatively abundant green water resources prevail across the study area. (3) Challenges related to water security stem from spatial and temporal mismatches between supply and demand of blue and green water resources. While blue water security is compromised in the agricultural agglomerations of the central area, spatial differences in green water security are less significant. These findings carry important implications for sustainable regional water resource management. Addressing the complexities of water security requires integrated approaches that consider both blue and green water resources, emphasizing the need for coordinated policies and strategies to ensure the equitable and sustainable use of water resources in the middle reaches of the Heihe River and similar regions worldwide.