Exploring the environmental problems based on ecosystem disservices is critical to achieving spatially explicit reasonable management measures. In this study, we adopted the methods of ecosystem disservice bundles to realize the division of small watersheds, replacing the traditional criterion of river buffers and slope. Firstly, we analyzed the bundles of seven ecosystem disservices, including sediment export, nitrogen and phosphorus pollution export, surface runoff, quick flow, and risks of collapse and debris flow at six small watersheds in the northwest of Beijing, where the water environment requires urgent improvement. Each ecosystem disservice bundle represented a class of function zone division in space. Based on the relative size of ecosystem disservices in bundles, we identified the main environmental problems in each class of the function zones. Finally, the management spaces were allocated in the spatial dimension according to the environmental problems. The results showed that the surface runoff was the most common environmental problem in all function zones. Additionally, the main environmental problems of the ecological restoration zones were the natural disasters and the sediment export. The environmental problems of the ecological management zones varied among the seven categories of ecosystem disservice bundles and mainly included the sediment export, the nitrogen pollution export, the phosphorus pollution export, and the quick flow. There were seven classes of function zones belonging to the ecological protection zones, of which the environmental problems of water pollution and quick flow required the greatest focus. Overall, the three management measures consisted of enclosure protection, rain (sewage) collection, and runoff regulation could be adopted to solve the environmental problems in the study area. Adopting both of the theory and the method of ecosystem disservice bundles can promote the detection of environmental problems and the achievement of spatial layout of management measures as well as the improvement of multiple ecosystem services at a landscape.