Natural springs, recognized as biodiversity hotspots and keystone ecosystems, exert positive ecological influences beyond their immediate extent, particularly in dryland environments. The water feeding these springs, largely governed by natural climatic conditions, is susceptible to anthropogenic impacts. The objective of this study was to determine the factors that cause fluctuations in water availability to springs of the hyper-arid Arava Valley (Israel/Jordan). Using the Standard Precipitation Index, we statistically classified the historical record of yearly rainfall for the past four decades into clusters of dry and wet sub-periods. We assessed changes in vegetation cover around the springs using the Landsat-derived Normalized Difference Vegetation Index (NDVI) for each sub-period. To assess the anthropogenic effects, we examined the correlations between vegetation cover, water extraction from the aquifer, and the status of adjacent agricultural plots that share a hydrological connection with the springs. Our findings revealed fluctuations between wet and dry sub-periods over the last four decades. We observed high responsiveness of vegetation cover around the springs to these fluctuating sub-periods. Of the 25 studied springs, 12 were directly influenced by anthropogenic factors—7 experienced a decline in vegetation, which we attributed to water extraction from the aquifers, while vegetation increase in 5 springs was attributed to water seepage from agricultural areas upstream. In conclusion, addressing vital habitats such as natural springs in arid drylands requires a holistic approach that integrates long-term climatic, ecological, and anthropogenic observations.