Riparian forests in natural desert oases are extremely vulnerable to water shortages; of late these shortages have been associated with climate change and with increased human-led water allocation. This study covers a hundred-year history (1876–2017) of riparian forest growth at the Ejina Oasis, which is located in the lower reaches of the Heihe River basin of northwestern China. We collected tree cores from Populus euphratica, which is the major tree species found in the Ejina riparian forests. These samples allowed us to chart variations in riparian forest growth and to examine correlations between tree growth and local precipitation, temperature, drought indices, groundwater depth, and runoff volume from the middle reaches of the river. We found that groundwater depth (groundwater being mainly recharged by runoff) is the major factor limiting tree-stem radial growth. We compared runoff reconstruction series from upper reaches and P. euphratica radial growth in the lower reaches. We found a period of greatly decreased growth (1942–1951); which seems to have been due to human water diversion. We note that mountain runoff increased after 2000, but that riparian forest growth didn’t increase in tandem; the water that would otherwise have supported the forests had been diverted. Our study provides a warning for future water resource planning and suggests the desirability of policies that will balance the needs of natural ecosystems (riparian forests) with the requirements of artificial ecosystems (croplands).