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ALBUQUERQUE, N.M.—The irrigation season is officially over for thousands of farmers in the heart of New Mexico.

Those growing crops in the Middle Rio Grande Valley didn’t have it as bad as farmers in other corners of the parched state, where the irrigation season lasted only a few weeks and wells were the only source of water.

Still, farmers in the valley face the same grim prospects heading into next year—forecasts for a dry winter, more limited allotments and legal wrangling.

“What we’re going to have to do is manage the water, whatever we have available to us from the storage and the native flows,” said Subhas Shah, the chief engineer for the Middle Rio Grande Conservancy District.

The district had been parceling out water on a rotating schedule since March 1 to ensure its canals would remain wet through Monday, which marked the close of the season.

By scheduling the water, Shah said the district was able to bank about 94,000 acre-feet of water at El Vado Reservoir in northern New Mexico. That will help supplement next season’s supplies.

The problem is the district is concerned its ability to store water in the future could be compromised by how the federal government manages the Rio Grande. The district is weighing in on a lawsuit New Mexico Attorney General Gary King filed earlier this year against the Bureau of Reclamation.

The state contends the agency wrongfully made 65,000 acre-feet of water stored at Elephant Butte Reservoir available for release to Texas. King has said the water rightfully belongs to New Mexico and that the agency’s actions were illegal and violated the interstate compact that governs how the river is divided among New Mexico, Colorado, Texas and Mexico.

The agency disputes the allegations and has asked a federal court to dismiss King’s complaint.

The Middle Rio Grande Conservancy District began holding back its share of irrigation water in September, knowing that any savings would become a valuable safety net the following year.

Rain in early October helped bolster the river’s natural flows, allowing farmers to irrigate through the end of the season, Shah said.

Farmers farther down the Rio Grande and those in southeastern New Mexico have been less fortunate.

Along the Pecos River, farmers have been relying on groundwater pumped throughout the summer to water their crops. They received less than half of the 3.2 acre-feet that were allotted last year.

Next year, they could see allotments dip below a single acre-foot. An acre-foot is about 326,000 gallons, enough to meet the annual water needs of one to two U.S. households.

“If you don’t have access to a supplemental well, you just really have a tough decision on your hands,” said Dudley Jones, manager of the Carlsbad Irrigation District, which serves about 660 farmers.

“For some people, it’s going to be hard to make it,” he said in an interview Tuesday.

The Carlsbad district currently has just 12,800 acre-feet of water stored in three upstream reservoirs.

“That’s as low as we’ve been in many, many years,” Jones said. “If you believe in the weather forecasts and the La Nina weather pattern, it’s not looking optimistic in 2012.”

Jones said the district has been looking for ways to save every drop, including sealing cracks in infrastructure at various points in its system.

The Elephant Butte Irrigation District along the southern portion of the Rio Grande is doing the same to limit evaporation and seepage of water from its system.

This year marked the shortest irrigation season on record for the Elephant Butte district, and officials said next year is shaping up to be just as short with predictions calling for enough water for just one month of irrigation.

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