Liquid and solid precipitation is abundant in the high elevation, upper reach of the Heihe River basin in northwestern China. The development of modern irrigation schemes in the middle reach of the basin is taking up an increasing share of fresh water resources, endangering the oasis and traditional irrigation systems in the lower reach. In this study, the response of vegetation in the Ejina Oasis in the lower reach of the Heihe River to the water yield of the upper catchment was analyzed by time series analysis of monthly observations of precipitation in the upper and lower catchment, river streamflow downstream of the modern irrigation schemes and satellite observations of vegetation index. Firstly, remotely sensed NDVI data acquired by Terra-MODIS are used to monitor the vegetation dynamic for a seven years period between 2000 and 2006. Due to cloud-contamination, atmospheric influence and different solar and viewing angles, however, the quality and consistence of time series of remotely sensed NDVI data are degraded. A Fourier Transform method – the Harmonic Analysis of Time Series (HANTS) algorithm – is used to reconstruct cloud- and noise-free NDVI time series data from the Terra-MODIS NDVI dataset. Modification is made on HANTS by adding additional parameters to deal with large data gaps in yearly time series in combination with a Temporal-Similarity-Statistics (TSS) method developed in this study to seek for initial values for the large gap periods. Secondly, the same Fourier Transform method is used to model time series of the vegetation phenology. The reconstructed cloud-free NDVI time series data are used to study the relationship between the water availability (i.e. the local precipitation and upstream water yield) and the evolution of vegetation conditions in Ejina Oasis from 2000 to 2006. Anomalies in precipitation, streamflow, and vegetation index are detected by comparing each year with the average year. The results showed that: the previous year total runoff had a significant relationship with the vegetation growth in Ejina Oasis and that anomalies in the spring monthly runoff of the Heihe River influenced the phenology of vegetation in the entire oasis. Warmer climate expressed by the degree-days showed positive influence on the vegetation phenology in particular during drier years. The time of maximum green-up is uniform throughout the oasis during wetter years, but showed a clear S-N gradient (downstream) during drier years.