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"The Syrian refugee emergency is highlighting one of Jordan's most pressing problems -- water," said Christian Snoad of Oxfam, in a joint statement with the British Red Cross.
"Solutions need to be found to deal with Jordan's water scarcity and this will need to be done as a matter of urgency.
"The Jordanian government will need... large-scale help from governments around the world to address this critical issue," said Snoad.
Jordan has taken in waves of Palestinian and Iraqis refugees who fled conflicts over the past few decades, and now hosts more than 450,000 Syrians, including 120,000 in the sprawling northern border camp of Zaatari alone.
The desert kingdom's "water supply system, already under severe strain, is being stretched to the limit by the large influx of refugees fleeing conflict in Syria," the statement said.
Faced with chronic water shortages, Jordan, whose own population has been growing at an annual rate of 3.5 percent, has been forced to extract more water from the ground since the mid-1980s.
More than 3,500 cubic metres of water are delivered each day into Zaatari, providing refugees with clean water for drinking, cooking and cleaning, said the statement.
"It's just a matter of time before the main sources run out. In some areas, groundwater extraction is nearly three times the recharge rate," it added.
Syrian refugees could afford to buy filtered water in Jordan, one of the world's 10 driest countries, where desert covers 92 percent of its territory.
"They have reported an increase in diarrhoeal cases among their young children who have no choice but to drink water straight from the tap, when it flows," said the joint statement.
"For its programme in Zaatari, Oxfam has adopted water-conservation measures such as taps that run water for short periods of time to prevent water wastage.
"Agencies have also called for the need to create better awareness among the refugee arrivals of Jordan's water problems."
Years of below-average rainfall have created a shortfall of 500 million cubic metres (17.5 billion cubic feet) a year, and the country forecasts it will need 1.6 billion cubic metres of water a year by 2015.