Scholars have long believed that a major drought caused severe dry conditions that killed off the ancient culture known for its mastery of language, math and astronomy.
But researchers from the Yucatan Center for Scientific Research in Mexico and the University of Southampton in Britain said their analysis shows the drought only caused reductions of 25 to 40 percent less annual rain.
The smaller amounts of rain meant that open water sources in pools and lakes evaporated faster than could be replaced by more precipitation, said the study in the journal Science.
"The data suggest that the main cause was a decrease in summer storm activity," said co-author Eelco Rohling of the University of Southampton.
The study is the first of its kind to attempt to assess exactly how much rainfall decreased between 800 and 950 AD when Mayan civilization went into decline, and bases its modeling data on records of past rainfall changes from stalagmites and shallow lakes.
The analysis showed that modest dry spells could have sparked major water shortages in an area with no rivers, and no source of water other than rain.
"Summer was the main season for cultivation and replenishment of Mayan freshwater storage systems and there are no rivers in the Yucatan lowlands," added Rohling.
"Societal disruptions and abandonment of cities are likely consequences of critical water shortages, especially because there seems to have been a rapid repetition of multi-year droughts."
International experts have predicted that similar dry spells in the Yucatan region are on the way due to climate change.
While modern societies are expected to be better equipped to handle drought, risks remain, said lead author Martin Medina-Elizalde of the Yucatan Center for Scientific Research in Mexico.
"Our results show rather modest rainfall reductions between times when the classic Maya civilization flourished and its collapse -- between AD 800-950. These reductions amount to only 25 to 40 percent in annual rainfall," he said.
"What seems like a minor reduction in water availability may lead to important, long-lasting problems. This problem is not unique to the Yucatan Peninsula, but applies to all regions in similar settings where evaporation is high."