The Heihe River basin consists of three different characteristic regions: upstream mountain area, midstream oasis region, and downstream desert region. Understanding the river–groundwater interactions in different river reaches is important for sustainable water resources management. In this study, river–groundwater interactions in three different river regions are investigated by the analysis of geophysical characteristics, meteor-hydrological characteristics, agricultural irrigations, and channel water balance equation in the river reaches in different seasons. Results indicate that the river–groundwater interactions vary geographically in the three different regions, and change seasonally with the strongest interactions during the summer. Groundwater discharges into the river in the upstream mountainous reach (annual 2.57 × 108m3) while the river water seeps into aquifers in the downstream desert reach (annual 10.39 × 108m3). In the midstream oasis region, pumping water for agriculture irrigation significantly affects the river–groundwater interaction. The river loses water to the ground during the major- and medium-irrigation periods, and gains water from groundwater during the minor-irrigation period in the midstream reach. The characteristics of the river–groundwater interactions are primarily dominated by physiographic features and precipitation in the upstream mountainous region, by human activities and precipitation in the midstream oasis region, and by evaporation and human activities in the downstream desert region.