Natural ecosystems in the region of the lower Tarim river in northwestern China, strongly deteriorated since the 1950s due to an expanding desertification. As a result, the downstream Tarim river reaches became permanently dry land. This historical evolution in land-use change is typically the result of the anthropogenic impact on natural ecosystems. Based on a spatially distributed hydrological catchment model bi-directionally linked with a fully hydrodynamic MIKE11 river model, land-use changes characterized by historical changes in leaf area index (LAI) of vegetation as well as the evolution of irrigated surface areas, can be causally related to changes in water resources (groundwater storage and surface water resources). An increased surface area of irrigated (agricultural) land together with a majority of inefficient irrigation methods, did lead to a strong increase of water resources consumption of the farmlands located in the upper Tarim river area. Evidently, this evolution influenced available water resources downstream in the Tarim basin. As a result, farmland has been gradually relocated to the upstream regions. This has led to reduced flows from the upper Tarim stream, which subsequently accelerated the dropping of the groundwater level downstream in the basin. This study moreover demonstrates that land surface biomass changes (cumulative LAI) along the lower Tarim river are strongly related to the changes in groundwater storage.