The ecological water conveyance project (EWCP) in the lower reaches of the Tarim River provided a valuable opportunity to study hydro-ecological processes of desert riparian vegetation. Ecological effects of the EWCP were assessed at large spatial and temporal scales based on 13 years of monitoring data. This study analyzed the trends in hydrological processes and the ecological effects of the EWCP. The EWCP resulted in increased groundwater storage-expressed as a general rise in the groundwater table-and improved soil moisture conditions. The change of water conditions also directly affected vegetative cover and the phenology of herbs, trees, and shrubs. Vegetative cover of herbs was most closely correlated to groundwater depth at the last year-end (R = 0.81), and trees and shrubs were most closely correlated to annual average groundwater depth (R = 0.79 and 0.66, respectively). The Normalized Difference Vegetation Index (NDVI) responded to groundwater depth on a 1-year time lag. Although the EWCP improved the NDVI, the study area is still sparsely vegetated. The main limitation of the EWCP is that it can only preserve the survival of existing vegetation, but it does not effectively promote the reproduction and regeneration of natural vegetation.