The BLM approved Gasco's project in November 2012; according to reports released by Gasco earlier this year, drilling was delayed as the company addressed stipulations to protect burrowing owls and golden eagles at or near the well sites.
The conservation organizations say the wells never should have been approved in the first place.
"The Pariette Wetlands ... are remarkable oases surrounded by high desert steppe," the suit states. "These wetlands are rich in wildlife and vegetation."
The wetlands support a waterfowl management area, the lawsuit notes. The environmental groups claim the drilling also would contribute to already high air pollution levels and possible water pollution.
The environmental groups are asking that the court order void the BLM permits for the project and order an injunction against drilling at the well sites.
Representatives from SUWA, The Wilderness Society, the BLM and Gasco could not be reached for comment Wednesday night.