There is a growing concern about the ecological conditions in the Haihe River which have been profoundly impacted by the growing human population and intensifying development over the past several decades. By identifying the spatial characteristics of terrestrial and fluvial landscapes, we propose the guidelines and criterions for regionalizing the freshwater ecosystems in the Haihe River basin. The first-level and second-level zones reflect the spatial patterns of the natural backgrounds which could impact the surface water quantity and quality. The 6 first-level zones are regionalized according to topographic characteristics, runoff depth, annual precipitation and evaporation. They represent the spatial pattern of water resource quantity. The 16 second-level zones are regionalized according to the vegetation and soil types overlaid by the first-level zones. They represent the spatial patterns of eco-hydrological processes and water purifying functions of terrestrial landscapes. Finally, the eco-regions are evaluated by the field survey data including water quality, aquatic vegetation and zoobenthos communities. This study could potentially be used to guide the decision-making process for the management of water resources and local ecological projects in the Haihe River basin. The methods formulated in this research can possibly provide important references for other watersheds in China.