Irrigated farmland dropped by 47 percent from 2013-2015, said the report published in the Proceedings of the National Academy of Sciences.
"The flight of refugees caused a significant reduction in farming, and therefore irrigation water use, in Syria," said the study led by researchers at Stanford University in California.
The study focuses on the Yarmuk-Jordan river watershed, which is shared by Syria, Jordan and Israel.
Since war conditions made it too difficult to study from the ground, researcher Jim Yoon decided to use satellite imagery processed in Google Earth Engine.
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Composite images of the 11 largest Syrian-controlled surface water reservoirs in the basin showed a 49 percent decrease in reservoir storage.
Meanwhile, the lack of green visible from the sky showed that irrigated land in the basin had decreased by 47 percent.
"It's the first time that we could do large-scale remote sensing analysis in a war zone to actually prove a causal relation between conflict and water resources," said lead author Marc Muller, a postdoctoral researcher in the lab of Steven Gorelick, a professor in Stanford's School of Earth, Energy and Environmental Sciences.
"The effects were so strong, it was really easy to see right away."
The war in Syria has killed more than 300,000 people since it started in March 2011 with a wave of anti-government protests.