ook at a map of North Africa from Egypt to Algeria. Almost everything outside the Nile Valley and south of the coastal plain appears to be lifeless sand and gravel deserts, spotted here and there with oases and rain-catching massifs of uplifted bedrock. But peer deeper, under the sand, and you will find water.

Under the Sahara lie three major aquifers, strata of saturated sandstones and limestones that hold water in their pores like a wet sponge. The easternmost of these, extending over two million square kilometers, underlies all of Egypt west of the Nile, all of eastern Libya, and much of northern Chad and Sudan, and contains 375,000 cubic kilometers of water—the equivalent of 3750 years of Nile River flow. It is called the Nubian Sandstone Aquifer System, and lately it has come to the attention of practitioners of a subspecialty of nuclear science known as isotope hydrology.

Isotope hydrology, which studies the atoms of the two elements making up groundwater—oxygen and hydrogen—and the trace elements in it, like carbon and nitrogen, is able to determine when, give or take a couple of thousand years, today’s groundwater fell to earth as rain. In the case of the Nubian Aquifer, some water in the system is thought to be one million years old, but most of it fell between 50,000 and 20,000 years ago at the time of the paleomonsoon. Since then, as the region has slowly turned to desert, especially during an acutely arid period from 20,000 to 12,000 years ago, there has been little addition of water to the aquifer. What lies beneath the ground is called fossil water, and it will likely never be replaced—or, in the parlance of hydrologists, the aquifer will never be recharged.

Because the Nubian Aquifer is shared among four nations, and because Libya and Egypt are now going forward with big water-pumping projects that tap the Nubian Aquifer, the International Atomic Energy Agency ( IAEA ), co-recipient of the 2005 Nobel Peace Prize, is trying to bring the countries together in a joint effort to plan for a rational shared use of the water.

Nuclear scientists are leading the way now, but sometime in the future diplomats may be signing aquifer-sharing treaties similar to those that now commonly control the sharing of surface waters. Such a treaty allots the Nile River’s flow among Ethiopia, Sudan and Egypt. Esmat Abdel Meguid, former secretary-general of the Arab League and Egyptian foreign minister, likes the sound of the words diplomacy and hydrology in the same sentence. “International agreements are the only way to go, especially among thirsty neighbors who live in the desert,” he says.

Dr. Aly Islam, chairman of the Egyptian Atomic Energy Authority ( EAEA ), whose isotope-hydrology laboratory in Cairo is a key asset in the project, has an even sharper perspective on the subject of “atoms for peace.” “Mankind’s use of nuclear science to date has been rather sad,” he says. “But if we who specialize in the atom can dedicate ourselves to peaceful ends, like water analysis, or seed research, or even irradiating semiprecious gems to make them more beautiful, then we will have done our part.” Dr. Islam is himself a world expert in the nitrogen-15 isotope, used for water-pollution studies.

The stakes are certainly high. Although the population density of the area overlying the aquifer is less than one person per square kilometer (2.6 people per square mile)—1/2000 that of the populous Nile Valley—desert agriculture and resettlement plans dating from the 1960’s are being dusted off. Egypt eventually hopes to use almost half a billion cubic meters of groundwater annually—more than the volume of Lake Erie. Libya is already pumping water from the Kufra Oasis, in its southeast corner, through a four-meter-diameter pipeline to its thirsty coastal cities. When fully operational, that project will pump some 3.6 million cubic meters per day. Still, at current extraction rates, the aquifer is not likely to be depleted for a thousand years.

Kufra lies not far across the border from Egypt’s East Uweinat agriculture project, which itself is just north of Sudan’s Salima Oasis, whose soils have proved high fertility. Farther north, Libya’s Al-Jaghboub Oasis and Egypt’s Siwa Oasis are pumping from the aquifer’s same limited sub-basin. Even northern Chad’s 3415-meter-high Tibesti Massif, where any development plans are far in the future, is critical to what little rainfall does recharge the aquifer in southern Libya and Egypt. In the region where the four countries touch, everything underground seems connected.

The EAEA ’s isotope hydrology lab, filled with high-tech machinery and directed by Dr. Sawsan Abd El-Samie, is a long way from the blazing desert. But water from that desert is tested here and compared to previously quantified international samples, supplied through the IAEA by the United States Geological Survey in tiny vials labeled with such far-off names as “Antarctic Water 1” and “Puerto Rico Water 1.” The machine that does the comparisons, an isotopic ratio mass spectrometer, is periodically recalibrated against the IAEA standard, known as VSMOW , or “Vienna Standard Mean Ocean Water.”

Abd El-Samie and her team go about the task of purifying and maximizing the component gases that she squeezes out of her water samples, using extreme heating and cooling and vacuum pressurizing to a tiny fraction of normal atmospheric pressure. “Sample purity is essential when we work at the atomic level,” she says, “and we must check and recheck for anomalies. Sometimes our irrigation-engineer colleagues do not understand why they must protect a sample against contamination—they think water is always just water.”

Abd El-Samie is looking for oxygen and hydrogen atoms with extra neutrons in their nuclei; such atoms act as markers, or fingerprints, for that particular sample and can give a relative timeline for the groundwater’s deposition. Water sampled at different depths acts almost like a rain-gauge record that goes back tens of thousands of years.

Another machine, the liquid scintillator, looks for the sample’s carbon-14 isotope, which attaches to water molecules in the sky when cosmic rays strike. Since carbon-14 is an unstable isotope with a known half-life, it can be measured and dated with some accuracy. But the scintillator is a thirsty machine: It usually takes a 60-liter water sample to yield just 300 milligrams of testable carbonate.

The project’s reach extends from the laboratory to the desert, with an intermediate stop at the Groundwater Research Institute, part of the National Water Research Center under Egypt’s Ministry of Water Resources and Irrigation. This is the core of the nation’s irrigation know-how, which stretches back some 5000 years. The center is located, appropriately, at the Nile Barrage just north of Cairo, where engineering works divide the two branches of the Nile and provide a testament to Egypt’s long history of manipulating the flow of water.

Dr. Taher Muhammad Hassan is charged with pulling together all the project’s many strands, from isotope laboratory results to piezometer (well-pressure) readings, from geological maps to the resettlement dreams of social policymakers. “We know some things about the Nubian Aquifer but many other things we do not,” he says. “The aquifer is what we call a closed system, but within it there are many internal dynamics—sub-basins and drainages, impermeable clay layers, vertical faults and horizontal fissures, and a limited potential for local recharge. And everything is deep underground, far out of sight.”

He gives the example of the Great Sand Sea, the dune system between Egypt and Libya west of Farafra Oasis. Eighteen-meter dunes overlie a layer of clay, which may hold a large isolated reservoir, a perched water table. Ground-penetrating radar indicates something is there, not far from the surface—but how to access it and, given the rough topography and poor soil conditions, why bother? “Not now,” says Hassan with a smile. “But maybe later.”

“One thing that isotope studies have shown us,” Hassan continues, “is that there is surprising little aquifer recharge from the Nile. Nile water has a younger isotopic profile, and samples from wells dug as close as five kilometers from the river show no sign of the Nile fingerprint. In fact, some of that well water is dated at 26,000 years old.” Since scientists now know they cannot rely on passive recharge taking place naturally, they might engineer it artificially, channeling water from the Toshka emergency spillway, just north of Abu Simbel, toward Kharga Oasis and helping it to enter the aquifer there by digging infiltration basins, injection (pumped) wells and gravity (percolation) wells.

“We had a huge Nile flood in 1996,” says Hassan, “and 33 billion cubic meters of river water filled the Toshka depression, just 50 kilometers from Kharga, where it has been evaporating ever since at a rate of three billion cubic meters each year. Now we have salt marshes there, good for duck hunting but not much else.”

Hassan is confident there is little likelihood of international conflict over aquifer sharing. “We know that the velocity of underground flow in most places is just two meters a day,” he says. “It’s like sucking a thick milkshake through a straw—it doesn’t happen fast, and eventually it stops completely.” Even Libya’s big extraction plans for Kufra will probably have only a minor effect on Egypt’s East Uweinat farming area, given the distance between the two. If Kufra’s water table drops 200 meters, the Egyptian side might see a drop of only 10 centimeters.

Such confidence does not travel very far, however. In the Bahariyya Oasis, a five-hour drive southwest of Cairo out past the Pyramids, the famous Roman spring called Bishmu has gone dry in recent memory due to over-pumping from nearby wells. The oasis has some 75 government-dug deep wells and hundreds of privately dug shallow wells. Because Bahariyya is a geological uplift, comprising limestone underlaid here by sandstone, some of the aquifer’s 30-odd horizons, or distinct water-bearing rock strata, are near the surface; some wells are thus free-flowing and require no mechanical lifting.

Sixty-five-year-old Abdel Min’am Hasaballah, who farms 12 feddans (roughly 12 acres) of wheat, barley, alfalfa and date palms, relies on a nearby 1000-meter-deep government well to allocate him 11 hours of water in each 15-day irrigation cycle, called a dawrah. Before the construction of the Aswan High Dam, his father dug a 100-meter free-flowing well which subsequently went dry in this long-farmed part of the oasis. Abdel Min’am blames the deep well’s hot 50°C (122°F) water for killing his apricot trees—which may be true—and also blames the dam for knocking the hydrology of the oasis off-kilter, which is less accurate.

More likely his father’s problem stemmed from the steady reclamation of thirsty new lands on the oasis’s margins. Not far away, Talaat Abdel Bari works as a contract well-digger, using the free-spinning wheel of an old tractor set on blocks to power a pipe-driving hammer. He charges small farmers $10 per meter of well depth ($3.05 per foot); by 70 meters’ depth he usually strikes water that will free-flow at a rate of 10 cubic meters per hour—just about right to irrigate this client’s eight feddans. Each feddan requires about 25 cubic meters per day, depending on the crop mix. Even if a well goes dry after five years of steadily decreasing flow, a farmer will have profited from the investment, and need only sink another well close enough to the first one to use the same irrigation channels.