The river Jordan is in danger of disappearing altogether under pressure from huge water diversion programs, an environmental group has warned.
The Dead Sea is also under threat of drying up.
More than 90% of the water is being diverted by Israel, Jordan and Syria, Friends of the Earth Middle East say.
The group have called on the governments in the region to take immediate action to save the river.
The river is also heavily polluted and now contains 20% untreated sewage, the organisation says.
The 1994 Israeli-Jordanian peace treaty obliges both governments to protect the Jordan "against any pollution, contamination or harm".
At a conference on an island on the river this week the Israeli, Palestinian and Jordanian governments recognised the scale of the problem, but promised no specific action to deal with it.
"We don't think this is good enough," Gidon Bromberg of Friends of the Earth Middle East told the BBC News website.
"In the last 10 years the governments have done nothing - in fact they've made the problem worse."
The river is already running dry in some areas and Friends of the Earth estimate that it could dry out completely within two years.
The pollution in the Jordan flows into the Dead Sea, which itself is under threat and has shrunk by 30% in the last 50 years.
Environmentalists want governments the United Nations to protect the river - a holy site for Christians, Jews and Muslims - by placing it on the UNESCO World Heritage list.
Israel currently diverts up to a third of its water supply from the Jordan, mainly for agricultural purposes.
Jordan also relies on dams on the river to irrigate land.
The Israeli Ministry of the Environment said in a recent statement that river restoration was a high priority.
"Tens of millions of dollars have been invested in restoring the country's ailing rivers and stringent enforcement against polluters has been carried out leading to over 163 indictments," the statement said.
Many analysts predict that scarce water resources will be one of core factors at the heart of conflict in the region.
Palestinians complain that Israel diverts up to 80% of water from shared underground aquifers for its own use - including that of Jewish settlers.