If Jesus were alive today, he might reconsider a baptism in the river Jordan; there’s a good chance he’d pick up an eye infection. Faecal bacteria in the pungent, murky waters have risen in recent years to up to six times the recommended levels.

Once a raging torrent, the lower Jordan has been starved of water to become a stagnant stream, filled with sewage and dirty run-off from farms. Around 95% of its historical flow has been diverted by agriculture during the past half-century. And the river’s primary source, the Sea of Galilee – where Christians believe the son of God walked on water – has for years been dammed to prevent its demise.

Biblical bodies of water in the Holy Land, eternalised in Christian, Jewish and Muslim ancient texts as godly, are now facing very human threats: climate change, mismanagement and conflict.

Following five consecutive years of drought, the Sea of Galilee has sunk to a 100-year low. A number of small islands have emerged at the water’s surface, and several holiday homes that were built on the shoreline now stand at least 100 metres from the boggy edge.

Overuse has also taken its toll. Last summer, the level of the lake dropped close to a black line, a level at which it could lose its status as a freshwater body. “The black line is our best guess of that point,” says Gidon Bromberg, the Israeli director of EcoPeace, an organisation of Israeli, Palestinian and Jordanian environmentalists. “It was tens of centimetres above the black line,” he says, adding that such a shallow depth has not been seen in records taken over the past century.

As the lake’s level falls, it cannot wash away salt fast enough, and its salinity rises. If the Sea of Galilee’s waters were left to hover around the black line, its flora and fauna would start to perish. A glimpse of the lake’s grim future might be seen 350km downriver at the lowest place on the planet: the Dead Sea, a body almost devoid of fish and plant life. “Once the lake becomes saline, that could be irreversible,” says Bromberg, speaking at the muddy edge of the water, reeds poking up behind him.

As Israel’s largest lake, the Sea of Galilee – which locals call the Kinneret, its Hebrew name – has long been the country’s main source of fresh water. But it cannot be relied on any more, says Yoav Barkay-Arbel, an engineer for Mekorot, the national water company. Standing at the Eshkol water pumping station on the peak of a hill, Barkay-Arbel looks across a series of reservoirs and intricate piping systems. Zionists in the early 1920s had intended to use the lake in the green, lush north to supply water to the arid south and “make the desert bloom”. A network of pipes from the Sea of Galilee, which is 214 metres below sea level, link to surrounding hills and then down towards the coast.

At its peak, the installation pumped hundreds of millions of cubic metres of water from Galilee to the rest of Israel. As fears grew that such volumes would deplete the lake, the plant has reduced to moving just 20m cubic metres per year. “That is zero. That is nothing. It’ll remain practically zero for the next couple of years,” says Barkay-Arbel, adding that Galilee supplies will now only be used in emergencies.

Facebook Twitter Pinterest Christians from around the world flock to the Sea of Galilee, where they believe Jesus walked on water. Photograph: Quique Kierszenbaum/The Observer

In a rush to save the lake, Israel is now looking at reversing the flow. Over the next few years it will spend millions of shekels moving seawater, desalinated at plants on the coast, 75km up to the Sea of Galilee.

Israel is a world leader in desalination, with five plants built along the Mediterranean coast. However, the Eshkol station was never meant to move water east instead of west. Open canals, built by engineers in the 1950s at a slight angle to improve water flow, still cut through the land. But they are at the wrong angle, and so a new pipe is being constructed along their side. “They never thought they would have to fill the lake with artificial water,” says Barkay-Arbel. “That is crazy. You cannot count on nature.” Nevertheless, the current plan is to be moving water in the next couple of years.

Saving the Sea of Galilee could, in turn, save the river Jordan, says Bromberg. He has campaigned to reopen the dam that blocks the lake from flowing into the Jordan. Without it, the river’s fragile ecosystem will deteriorate drastically and it could turn into a dry river bed. Five years ago, Israel agreed to release 9m cubic metres from the Sea of Galilee, a tiny amount of water, the first time its waters had run uninterrupted into the river since the 1960s. But hundreds of cubic metres will be needed to fully rehabilitate the river.

The source of the river is now a small creek, with two pipes each less than half a metre wide that pump out water. A third pipe releases yellowish liquid. This is treated sewage – not ideal, Bromberg says, but better than nothing.

As long as the Sea of Galilee is under threat, the river Jordan will be too. And their eventual deaths could have explosive ramifications as water in this region has been a key source of conflict. The river Jordan is shared by Israel, the occupied Palestinian territories, Jordan and Syria, all of which use its depleting reserves.

Facebook Twitter Pinterest Islands have become exposed as water levels fall. Photograph: Ahmad Gharabli/AFP/Getty Images

“Israel takes half, Syria and Jordan take the other half,” says Bromberg. “Because it’s a war zone, they take everything … The mindset of conflict leads to the complete demise of the river Jordan.”

In 2000, Syria’s then president, Hafez al-Assad, father of the current president, Bashar, turned down a deal to end three decades of on-off war on the basis that Israel refused to give him back access to the north-eastern shore of the Sea of Galilee. The prime minister at the time, Ehud Barak, ran on the campaign slogan: “No Syrian soldiers will splash their feet in the Kinneret.” Israeli forces had taken over the entire area in 1967.

Israel has retained hold of all the water resources in the Palestinian territories, where residents suffer regular shortages and often have to pay large amounts for private water lorry deliveries. In Gaza, which is under a tight Israeli-Egyptian blockade, most water is unsafe to drink.

“While Israel has become a trailblazer in the field of water technology, the failure to reach a fair water allocation and management agreement between Israelis and Palestinians is putting the Palestinian water sector under huge stress and continues to breed animosity that will only accelerate under climate change,” says a recent report by EcoPeace.

Israel also relied on the Sea of Galilee’s waters to forge a 1994 peace treaty with Jordan, agreeing to pump 55m cubic metres a year to its former enemy. That continues today, a deal that cannot be broken without diplomatic fallout, making the desalination project ever more critical.

EcoPeace hopes that good water management will spur on peace to the region. Bromberg is now advocating for a deal in which Israel, which is on the Mediterranean, supplies desalinated water to Jordan. In exchange, Jordan, which is low on water but full of open desert with 320 sunny days a year, will supply solar power.

Facebook Twitter Pinterest Ethiopian pilgrims in the polluted Jordan river at the site considered the place where Jesus was baptised by John the Baptist. Photograph: Quique Kierszenbaum

In the meantime, the river Jordan remains polluted. Most Christian pilgrims who want to be baptised in the holy waters do not venture to the original site where John the Baptist is believed to have led Jesus into the water. That location is in the occupied Palestinian territories next to Jordan, and the Israeli army mined it decades ago. Pilgrims were only allowed to return some years ago.

Authorities have instead promoted another attraction about 110km north in Israel. The Yardenit baptismal site was built in the early 1980s and welcomes half a million visitors each year. Here the water is clean as it is pumped from the Sea of Galilee into a holding area. Bromberg calls it a “man-made swimming pool”. Dozens of people in white gowns wait in line, walking through metal fences into the water, before being plunged below. A colossal gift shop sells bibles and religious trinkets, and customers can buy small bottles filled with water and stones from the plunge pool – three for 57 shekels, or around £12. Visitors can buy or rent white gowns for baptisms. A cafe outside sells ice-cream.

One day, the masses may return to the original site. And as the end of the winter approaches, authorities say an unusually rainy season has given the Sea of Galilee some relief and broken a five-year drought. As the snow melts in the north, they hope the water level will continue to rise.

But a rainy winter goes against the trend, and in a few short months the hot summer will evaporate the lake again, possibly taking it back down or below the black line. “It would be an ecological disaster,” says Bromberg.

• This article was amended on 24 February 2019. An earlier version stated that, at the peak, billions of cubic metres of water were pumped from Galilee to the rest of Israel. This has been corrected.