Elephant Butte Irrigation District officials announced this will be the worst water year in a century.
Delicious New Mexico-grown crops like pecans and chiles could be at risk.
Farmers have seen some small water allotments in the past few years. District officials said they need to start planning for the worst.
"It's a rough year. There's no question about it. It's bad as it's ever been in terms of the water supply," said Phil King, EBID water engineer.
Just a month ago, the outlook for this year's water was a bit brighter.
"I was anticipating that we would have enough water to make an allotment to EBID farmers of somewhere between 4 and 6 inches. That was making some assumptions about runoff that would come in. Even taking a pretty pessimistic view of the runoff that would be coming in between then and now, it was an overestimate," King told ABC-7.
King said the district saw just 12 percent of its normal spring runoff.
Low runoff paired with years of drought has left the district with the smallest amount of water to distribute.
Thousands of farmers throughout southern New Mexico, El Paso and Mexico will have to rely on groundwater.
"It affects different farmers very differently. Farmers near Hatch lack deep groundwater reserves so they're already starting to feel loss of capacity in groundwater wells. More importantly, they're seeing an increase in the salinity," King said.
High levels of salinity could be an issue for New Mexico's most important crops.
"The onions, chile and crops they grow up there are going to be negatively affected by the salt. Those are big revenue losers. Those are very valuable crops. In the Mesilla Valley, we do have a robust aquifer, so farmers who can manage to do so will pump most of their water supply," King said.
Irrigation officials predict farmers will get between 3.2 and 3.6 acre-inches of water for the entire spring and summer seasons.