Martin LaMonica/CNET

FARMINGTON, N.M.--Viewing the San Juan basin by air is one of the most dramatic ways to see where your energy comes from.

I got a chance to tour a portion of the basin on a small plane run by EcoFlight two weeks ago as part of a fellowship organized by the Institutes of Journalism & Natural Resources (IJNR). While most people have a vague idea of how energy is produced, the quick trip brought to life the footprint of large-scale energy production.

The Four Corners area in northern New Mexico is one of the country's most productive energy regions, featuring two very large coal power plants and about 30,000 natural gas wells.

From the air, you can quickly see what huge operations coal plants are, just from the giant plumes of steam in the air and the impact of coal mining done on site.

Individually, the natural-gas well pads dotted along the ground are far less dramatic. But the density of the drilling and the proximity to agriculture and residential areas was remarkable to me. There are an estimated 30 well pads per mile in the area, linked by many roads that crisscross the desert habitat.

At a local level, coal and natural gas are controversial for environmental and health reasons, including worries over the impact on water from hydraulic fracturing--known as "fracking"--and horizontal drilling. But as mainstays of the global energy system, coal and natural gas are deeply entrenched in the U.S.

Burning coal is the cheapest way to produce electricity, and the increased use of fracking here and other parts of the country has led to surge in domestic natural-gas production and lower gas prices. Those low fossil fuel prices continues to make it difficult for renewable sources such as solar and wind to compete without subsidies and gain market momentum.

Decades of fracking

Getting natural gas from so-called unconventional sources, such as shale rock or coal seams, has dramatically changed the energy picture for the U.S. in just the last few years. Hearing the local opposition to drilling practices, though, is a reminder of how all energy sources have strings attached.

The source for natural gas in the San Juan basin is coal bed methane, or gas trapped in coal seams rather than an underground reservoir. Drillers have been using fracking and horizontal drilling in coal for years, the same technique that's being used on shale rock in other parts of the country. These techniques have allowed the region to remain productive years after many wells were expected to dry up, according to Wally Drangmeister, the director of communications for the New Mexico Oil & Gas Association.

"The basin has been productive for decades and the technology continues to improve in very significant ways," he said. "Just when you're at the point where you think the basin will begin to taper off, new technologies and processes take off."

In addition to being domestic, natural gas emits about half the carbon dioxide coal does when burned, and it emits far less conventional air pollution. But for Gwen Lachelt, the executive director of EarthWorks Oil & Gas Accountability Project, natural gas is a dirty fuel, not a cleaner "bridge" fossil fuel to renewable sources.

One of the biggest areas of contention is the impact on water from fracking and horizontal drilling, Lachelt said, adding that her group regularly gets calls from people whose water supplies have been affected by nearby drilling.

In hydraulic fracturing, drillers pump water and a mix of chemicals into wells at high pressure to create fissures in underground rock that then release methane. Some of that pumped solution can be retrieved and, in the San Juan basin area, reinjected in other wells or trucked out, explained Drangmeister. Such drilling also produces brackish underground water that has to be disposed of.

In a desert area that sees less than ten inches of rain a year, water disposal and the fluids used during fracking are both big concerns. The EarthWorks Oil & Gas Accountability Project is pushing for mandatory disclosure of fracking chemicals, regulations on disposal of water from drilling, and requirements for drillers to capture methane gas, rather than flaring it.

There are also questions over how public lands are leased for minerals extraction and what rights communities have in an area of intensive energy exploitation. Local groups are organizing over concern to their local environment, but it's really part of a larger discussion on national energy use, Lachelt said, who advocates federal regulations on hydraulic fracturing.

"We have to have a serious discussion about the role of natural gas in this country--we can't take it for granted," she said. "If it's going to continue being part of the energy mix, we need to deal with it responsibly and have that conversation."