Poverty, repression, decades of injustice and mass unemployment have all been cited as causes of the political convulsions in the Middle East and north Africa these last weeks. But a less recognised reason for the turmoil in Egypt, Tunisia, Algeria, Yemen, Jordan and now Iran has been rising food prices, directly linked to a growing regional water crisis.

The diverse states that make up the Arab world, stretching from the Atlantic coast to Iraq, have some of the world's greatest oil reserves, but this disguises the fact that they mostly occupy hyper-arid places. Rivers are few, water demand is increasing as populations grow, underground reserves are shrinking and nearly all depend on imported staple foods that are now trading at record prices.

For a region that expects populations to double to more than 600 million within 40 years, and climate change to raise temperatures, these structural problems are political dynamite and already destabilising countries, say the World Bank, the UN and many independent studies.

In recent reports they separately warn that the riots and demonstrations after the three major food-price rises of the last five years in north Africa and the Middle East might be just a taste of greater troubles to come unless countries start to share their natural resources, and reduce their profligate energy and water use.

"In the future the main geopolitical resource in the Middle East will be water rather than oil. The situation is alarming," said Swiss foreign minister Micheline Calmy-Rey last week, as she launched a Swiss and Swedish government-funded report for the EU.

The Blue Peace report examined long-term prospects for seven countries, including Turkey, Iraq, Jordan, the Palestinian territories and Israel. Five already suffer major structural shortages, it said, and the amount of water being taken from dwindling sources across the region cannot continue much longer.

"Unless there is a technological breakthrough or a miraculous discovery, the Middle East will not escape a serious [water] shortage," said Sundeep Waslekar, a researcher from the Strategic Foresight Group who wrote the report.

Autocratic, oil-rich rulers have been able to control their people by controlling nature and have kept the lid on political turmoil at home by heavily subsidising "virtual" or "embedded" water in the form of staple grains imported from the US and elsewhere.

But, says Jon Alterman, director of the Middle East programme at the Washington-based Centre for Strategic Studies, existing political relationships are liable to break down when, as now, the price of food hits record levels and the demand for water and energy soars.

"Water is a fundamental part of the social contract in Middle Eastern countries. Along with subsidised food and fuel, governments provide cheap or even free water to ensure the consent of the governed. But when subsidised commodities have been cut, instability has often followed.

"Water's own role in prompting unrest has so far been relatively limited, but that is unlikely to hold. Future water scarcity will be much more permanent than past shortages, and the techniques governments have used in responding to past disturbances may not be enough," he says.

"The problem will only get worse. Arab countries depend on other countries for their food security – they're as sensitive to floods in Australia and big freezes in Canada as on the yield in Algeria or Egypt itself," says political analyst and Middle East author Vicken Cheterian.

"In 2008/9, Arab countries' food imports cost $30bn. Then, rising prices caused waves of rioting and left the unemployed and impoverished millions in Arab countries even more exposed. The paradox of Arab economies is that they depend on oil prices, while increased energy prices make their food more expensive," says Cheterian.

The region's most food- and water-insecure country is Yemen, the poorest in the Arab world, which gets less than 200 cubic metres of water per person a year – well below the international water poverty line of 1,000m3 – and must import 80-90% o f its food.

According to Mahmoud Shidiwah, chair of the Yemeni water and environment protection agency, 19 of the country's 21 main aquifers are no longer being replenished and the government has considered moving Sana'a, the capital city, with around two million people, which is expected to run dry within six years.

"Water shortages have increased political tensions between groups. We have a very big problem," he says.

Two internal conflicts are already raging in Yemen and the capital has been rocked by riots this month. "There is an obvious link between high food prices and unrest [in the region]. Drought, population and water scarcity are aggravating factors. The pressure on natural resources is increasing, and the pressure on the land is great," said Giancarlo Cirri, the UN World Food Programme representative in Yemen.

"If you look at the recent Small Arms Survey [in Yemen], they try to document the increase in what they call social violence due to this pressure on water and land. This social violence is increasing, and related deaths and casualties are pretty high. The death tolls in the northern conflict and the southern conflict are a result of these pressures," said Cirri.

Other Arab countries are not faring much better. Jordan, which expects water demand to double in the next 20 years, faces massive shortages because of population growth and a longstanding water dispute with Israel. Its per capita water supply will fall from the current 200m3 per person to 91m3 within 30 years, says the World Bank. Palestine and Israel fiercely dispute fragile water resources.

Algeria and Tunisia, along with the seven emirates in the UAE, Morocco, Iraq and Iran are all in "water deficit" – using far more than they receive in rain or snowfall. Only Turkey has a major surplus, but it is unwilling to share. Abu Dhabi, the world's most profligate water user, says it will run out of its ancient fossil water reserves in 40 years; Libya has spent $20bn pumping unreplenishable water from deep wells in the desert but has no idea how long the resource will last; Saudi Arabian water demand has increased by 500% in 25 years and is expected to double again in 20 years – as power demand surges as much as 10% a year.

The Blue Peace report highlights the rapid decline in many of the region's major water sources. The water level in the Dead Sea has dropped by nearly 150ft since the 1960s. The marshlands in Iraq have shrunk by 90% and the Sea of Galilee (Lake Kinneret) is at risk of becoming irreversibly salinised by salt water springs below it.

Meanwhile, says the UN, farm land is becoming unusable as irrigation schemes and intensive farming lead to waterlogging and desalination.

Some oil-rich Arab countries are belatedly beginning to address the problem. Having drained underground aquifers to grow inappropriate crops for many years, they have turned en masse to desalination. More than 1,500 massive plants now line the Gulf and the Mediterranean and provide much of north Africa and the Middle East's drinking water – and two-thirds of the world's desalinated water.

The plants take salty or brackish water, and either warm it, vaporise it and separate off the salts and impurities, or pass it through filters. According to the WWF, it's an "expensive, energy intensive and greenhouse gas-emitting way to get fresh water", but costs are falling and the industry is booming.

Solar-powered plants are being built for small communities but no way has been found to avoid the concentrated salt stream that the plants produce. The impurities extracted from the water mostly end up back in the sea or in aquifers and kill marine life.

Only now are countries starting to see the downsides of desalination. Salt levels in the Arabian Gulf are eight times higher in some places than they should be, as power-hungry water plants return salt to an already saline sea. The higher salinity of the seawater intake reduces the plant's efficiency and, in some areas, marine life is suffering badly, affecting coral and fishing catches.

Desalination has allowed dictators and elites to continue to waste water on a massive scale. Nearly 20% of all Saudi oil money in the 1970s and 80s was used to provide clean water to grow wheat and other crops in regions that would not naturally be able to do so. Parks, golf courses, roadside verges and household gardens are all still watered with expensively produced clean drinking water. The energy – and therefore water – needed to keep barely insulated buildings super-cold in Gulf states is astonishing.

A few Arab leaders recognise that water and energy profligacy must be curbed if ecological disaster is to be avoided. In Abu Dhabi, which is building Masdar, the $20bn futuristic city to be run on renewable energy, the environment agency is spearheading a massive drive to reduce water use. Concrete is replacing water-hungry grass verges and new laws demand water-saving devices in all buildings.

"We cannot go on giving free water and energy. It's not benefiting anyone. We have to change and we will change. We know we must find common solutions," says Razan Khalifa al-Mubarak, assistant head of the environment agency.

"Allah does not like those who waste," says Talib al-Shehhi, director of preaching at the ministry of Islamic affairs. "Safeguarding resources and water especially is central to religion. The Qu'ran says water is a pillar of life and consequently orders us to save [it], and Muhammad instructs us to do so."

Water awareness is definitely growing, says Kala Krishnan, member of an eco club at the large Indian school in Abu Dhabi. "People were amazed when we showed them how much they use in a day. We stacked up 550 one-litre bottles and they refused to believe it. Now schools are competing with each other to reduce water wastage."

More than 2,000 mosques in Abu Dhabi have been fitted with water-saving devices, which is saving millions of gallons of water a year when people wash before prayer. Other UAE states are expected to follow.

The more drastic response to the crisis is to shift farming elsewhere and to build reserves. Saudi Arabia said in 2008 it would cut domestic wheat output by 12.5% a year to save its water supplies. It is now subsidising traders to buy land in Africa. Since the troubles in Egypt and north Africa, it has said it aims to double its wheat reserves to 1.4m tonnes, enough to satisfy demand for a year.

Countries now recognise how vulnerable they are to conflict. The UAE, which includes Abu Dhabi and Dubai, has started to build the world's largest underground reservoir, with 26,000,000m3 of desalinated water. It will store enough water for 90 days when completed. The reasoning is that the UAE is now wholly dependent on desalination to survive.

"Wars can erupt because of water," said Mohammed Khalfan al-Rumaithi, director general of the UAE's National Emergency and Crisis Management Authority last week. "Using groundwater for agriculture is risky. If it doesn't harm us it will harm other generations," he told the Federal National Council.

"We suffer from a shortage of water and we should think about solutions to preserve it rather than using it for agriculture," he said.

Water shortages, concludes the Blue Peace report, are now so alarming that in a few years opposing camps will have little choice but to co-operate and share resources, or face ruinous conflict. That way, it says, instead of a potential accelerator of conflict, the water crisis can become an opportunity for a new form of peace where any two countries with access to adequate, clean and sustainable water resources do not feel motivated to engage in a military conflict. It sounds optimistic, but the wind of change blowing through the region suggests everything is possible.