LAKE POWELL, Utah—In early September, at the abandoned Piute Farms marina on a remote edge of southern Utah's Navajo reservation, we watched a ten-foot (three-meter) waterfall plunging off what used to be the end of the San Juan River.

Until 1990, this point marked the smooth confluence of the river with Lake Powell, one of the largest reservoirs in the U.S. But the lake has shrunk so much due to the recent drought that this waterfall has emerged, with sandy water as thick as a milkshake.

My partner DeEdda McLean and I had come to this area west of Mexican Hat, Utah, to kayak across Lake Powell, a reservoir formed by the confluence of the San Juan and the Colorado Rivers and the holding power of Glen Canyon Dam, which lies just over the border in Arizona. Yet in place of a majestic reservoir, we saw only the thin ribbon of a reemergent river channel, which had been inundated for most of the past three decades by the lake. We called this new channel the San Powell, combining the name of the river and the lake.

We had also come to see firsthand how drought is changing the landscapes of the desert Southwest. Here, judging by the lack of conservation reform, water has seemed to be largely taken for granted. But our recent float suggests that profound changes may be in store for the region. (See "The American Nile.")

Sweating in the desert heat, we loaded our 15-foot (5-meter) kayaks with two weeks' worth of food and ten gallons of water—enough to last us two days. Drinking from the silty river or fecal-contaminated areas of Lake Powell frequented by houseboats was not an option (Glen Canyon Recreation Area, which includes the reservoir, is visited by more than two million people a year). The contours of our journey—where we camped, our hiking destinations, and how far we paddled each day—would be defined by the need to find potable springs.

Like bicyclists shunning the interstate, many kayakers have avoided Lake Powell ever since the builders of Glen Canyon Dam finished flooding 186 miles (300 kilometers) of the Colorado River Valley in 1980. The reservoir was named after John Wesley Powell, the National Geographic Society co-founder who first paddled most of the Colorado River and who later, in public office, tried to limit population growth in the arid Southwest. The dams and the enormous reservoirs that were later built in the desert would have horrified him.

Motorboaters call Powell's lake the "Jewel of the Colorado" because of its unnatural emerald hue—Glen Canyon Dam now captures the silt that used to make the Colorado, after its confluence with the San Juan, the most colorful river in the West. Paddlers call it "Lake Foul" for the noise and stench of outboard engines.

"Extreme" Drought

According to the U.S. Drought Monitor, 11 of the past 14 years have been drought years in the Southwest, with the drought ranging from "severe" to "extreme" to "exceptional," depending on the year and the area.

At "full pool," Lake Powell spans 254 square miles (660 square kilometers) —a quarter the size of Rhode Island. The lightning bolt-shaped canyon shore stretches 1,960 miles (3,150 kilometers), 667 miles (1,073 kilometers) longer than the West Coast of the continental United States.

The reservoir serves multiple purposes. It stores water from the Upper Basin states of Wyoming, Utah, New Mexico, and Colorado so that the Lower Basin states of California, Nevada, and Arizona can receive their allotted half of the Colorado River; it creates electricity through hydro-generators at Glen Canyon Dam; and it helps prevent flooding below Hoover Dam (240 miles or 390 kilometers downstream), the site of North America's largest reservoir, Lake Mead.

The irony, as most students of this river's history now know, is that the U.S. Bureau of Reclamation created these enormous reservoirs during the wettest period of the past millennium. According to modern tree-ring data (unavailable during the dam-building epoch), the previous millennium experienced droughts much more severe than those in the first 14 years of the 21st century. Many climate scientists think the Southwest is again due for a megadrought. The Bureau of Reclamation's analysis of over a hundred climate projections suggests the Colorado River Basin will be much drier by the end of this century than it was in the past one, with the median projection showing 45 percent less runoff into the river.

Last winter was snowy in the Rockies, and runoff was at 96 percent of the historical average. Because of the previous years of drought, however, Lake Powell had risen to only half full by fall.

But Lake Mead was in even worse shape. This year it plunged to 39 percent of capacity, a low that has not been matched since Hoover Dam began backing up the Colorado River in 1935. In August, the Bureau of Reclamation announced that Lake Powell would release an additional 10 percent of its waters, or 2.5 trillion gallons, to Lake Mead. That release will lower the water in Lake Powell by about three feet (one meter).

Rise of Ancient Ruins?

Fifty miles (80 kilometers) up from the Colorado River confluence, on what is commonly known as the San Juan River Arm of Lake Powell, we kept poking our paddles-cum-measuring sticks toward the shallow river bottom, shouting: "Good-bye, reservoir! Hello, San Powell River!" In a four-mile-per-hour, opaque current, always hunting for the deepest river braids, we breezed past fields of still-viscous, former lake-bottom silt deposits. Stepping out of the boat here would have been an invitation to disappear in quicksand.

We paddled downstream, looking for the edge of the reservoir. We passed caterwauling great blue herons, a yipping coyote, and squawking conspiracies of ravens. By late afternoon, dehydrated by the desert sun, we stopped at one of the few quicksand-free tent sites above the newly emerged river: a sandy yet dry creek bed draining the sacred Navajo Mountain.

We slept in the perfume of blooming nightshades; wild burros brayed throughout the night. Here, more than a dozen miles below our put-in at a marina that once served the reservoir, the swirling "San Powell" River continued to sigh 15 feet (5 meters) below our tent.

In October 2011, when the reservoir was at 70 percent of its capacity, I had stood on a rocky shore above where our tent now stood and photographed Lake Powell's Zahn Bay here in the San Juan River Valley. It's dry now, and the lake bottom is a cracked series of chocolate-colored hummocks, surrounded by the invasive Russian thistle and tamarisk, native willows and sunflowers, and pockmarked by burro hooves.

For five days, we wouldn't see a human footprint or hear the ubiquitous whine of Lake Powell boat traffic.

Half full, the amazing vessel that is Lake Powell has lost 4.4 trillion gallons of water in the recent drought.

By day three, desperate to refill our water bottles, we found a newly created marsh where the river thinned before dropping into the deeper reservoir. Unlike anything I'd experienced elsewhere on the sterile Lake Powell, abundant small fish and aquatic life supported American pelicans, mallards, coots, mergansers, green herons, hawks, and kingfishers. The silty river is also sheltering endangered razorback suckers and pikeminnows that are preyed upon by non-native fish in the clearer waters of the lake.

Within a decade or two at the most, if the drought persists, we can expect to see hundreds of inundated ancient Anasazi ruins rising above the drying reservoir. Archaeologists will be delighted, just as kayakers like us delight at the reemergence of a river. But more than 36 million people in and around the Colorado River Basin depend on this vanishing water.

As we finally reached a body of water wide enough to be properly called the reservoir, many miles below where we had expected to find it, we continued paddling in a chocolate pudding of ground-up river debris. Some 94 feet (29 meters) above our craned heads, on the red sandstone walls of the reservoir, we saw the "bathtub rings"—the stains left by river minerals in wetter times.

That night we did a quick calculation: Half full, the amazing vessel that is Lake Powell has lost 4.4 trillion gallons of water in the recent drought; the deeper vessel of Lake Mead at 39 percent capacity has lost 5.6 trillion gallons of water.

As central California (beyond the reach of Colorado River water) has already been hamstrung by an even more exceptional drought, many farms and dairy operations have shut down, rationing has begun, homeowners are being fined for watering their lawns, and the state has begun relying on finite groundwater supplies. And as extensive farm networks are served by the Colorado River, it is likely that nationwide produce prices will soon begin to rise.

What's next? As Lakes Powell and Mead continue to plummet, officials are now predicting rationing by 2017 for the junior Colorado River water-rights holders of Nevada and Arizona.

In the decades that follow, invasive flora and fauna will colonize dried-out reservoir bottoms. River running and reservoir boating may end. Those will seem like minor issues compared with the survival of cities like Los Angeles, Denver, Phoenix, and Las Vegas, all of which depend on the Colorado River. There is talk of diverting more water to the Colorado Basin users from places such as the Missouri River. A massive desalination plant is being built on the California coast. But such solutions won't come cheap.

Officials are now predicting rationing by 2017 for the junior Colorado River water-rights holders of Nevada and Arizona.

We can hope for agricultural reform, such as irrigation changes, more aggressive crop rotation and fallowing, reverting to less water-intensive produce, or dismantling of the water-intensive southwestern dairy industry. And the exponential population growth of the region—as Powell warned at the end of the 19th century—will have to be addressed. (See "Arizona Irrigators Share Water With Desert River.")

By mid-September, we reached the speedboat-accessible region of Lake Powell. Motorboaters often stopped to ask if we needed help. Many of these boaters offered us iced beer or bottled water imported from distant regions of the country.

Each day, for 14 days, except during two violent but brief rainstorms, the temperature climbed into the 90s. Often dizzy, and even exhausted from the heat, we parceled out our water, cup by cup, consuming over four gallons daily. And every other day, we walked or paddled miles out of our way so that we could enact a time-honored practice of desert cultures like the Anasazi's, which vanished in the 13th-century megadrought.

Every other day, we uncapped our empty bottles while honoring this ritual of aridity: Bowing under shaded cliffs at moss-covered seeps, we pressed our lips onto cold sandstone walls and drank those precious drops until our bellies were full.

Jonathan Waterman is a writer and photographer based in Colorado. In 2010 National Geographic published his book Running Dry: A Journey From Source to Sea Down the Colorado River. He is also the co-author, with Pete McBride, of The Colorado River: Flowing Through Conflict. See his previous work "The American Nile."