In the early 1960s, the river moved 1.3 billion cubic metres of water every year from the Sea of Galilee to the Dead Sea.
But dams, canals and pumping stations built by Israel, Jordan and Syria to divert water for crops and drinking have reduced the flow by more than 90% to about 100 million cubic metres.
"The Jordan river will disappear if nothing is done soon. More than half of it is raw sewage and runoff water from agriculture. What keeps the river flowing today is sewage," said Munqeth Mehyar, chairman of Friends of the Earth Middle East (FOEME), an Israeli-Jordanian-Palestinian group.
Next month, FOEME says it will host an event in which Israeli, Jordanian and Palestinian mayors will jump into the Jordan as part of a campaign to clean up the dying river.
The dramatic decline in the Jordan is the main reason why the Dead Sea is also vanishing. The level of the world's saltiest large body of water is falling by a metre each year and the sea could disappear in 50 years, experts say.
"The Jordan river will disappear if nothing is done soon. More than half of it is raw sewage and runoff water from agriculture. What keeps the river flowing today is sewage"
Chairman, Friends of the Earth Middle East
Years of conflict between the main users of the river - revered by Christians, Muslims and Jews - have contributed to the crisis. The river meanders for 200km along the lush Jordan Valley, separating Jordan, Israel and the West Bank.
"The story of the demise of the River Jordan is the competition between Israel, Jordan and Syria for water. It is about grabbing as much water as they possibly can," said Gidon Bromberg, FOEME's Israeli director.
Almost all the tributaries that feed into the river have been dammed or diverted, turning the Jordan - believed to have been the gateway to the Garden of Eden - into an insalubrious stream in some parts, especially in summer.
In the 1950s, Israel built a pipeline to pump water out of the Sea of Galilee, stopping its flow into the Jordan, said Bromberg.
Jordan then constructed a canal in the 1970s to divert water out of the Yarmuk River, a main tributary of the Jordan, to water its farmland, said Mehyar, a Jordanian.
A dam being built by Jordan and Syria on the Yarmuk will cut off all its flow into the Jordan, they said.
The 1994 peace treaty between Jordan and Israel called for the rehabilitation of the river, but little has been done.
Pollution does not seem to bother the pilgrims who come from around the world to the river's fabled banks to fill souvenir bottles with muddy water.
"People should not be allowed to dip in the river. It is anything but holy water"
FOEME's Israeli director
In the baptismal site of Bethany Beyond the Jordan, on the Jordanian side, officials have built pools where treated water is pumped to allow pilgrims to bathe in cleaner waters.
But some risk-takers dip in the greenish river itself. "It is a health hazard. People should not be allowed to dip in the river. It is anything but holy water," said Bromberg.
He said half of Israel's fresh water is used for agriculture. "We are not asking governments to put all the water back but to strike a better balance between water resources and the ecological and historical importance of the river," he said.
FOEME says the river should be designated a Unesco world heritage site.