The San Juan Watershed Group and the Animas Watershed Partnership will present their findings to city council at 9 a.m. on Tuesday.
The Animas River exceeds the threshold for nutrient levels, said David Tomko, watershed coordinator for the San Juan Watershed Group.
High nutrient levels cause algae and weed growth, which can ruin water quality and harm fish.
E. Coli and sediment levels in the Animas River are also above U.S. Environmental Protection Agency thresholds, he said.
The San Juan River had been listed for bacteria until January 2012, Tomko said, while the Animas River had not previously been listed in that category.
The La Plata River may be the worst off.
It exceeded EPA thresholds for bacteria, nutrients and temperature, most likely because of its low water level, Tomko said.
Working together, the two river conservation groups found two categories of contaminants in local rivers.
The first are point sources, such as discharge from a wastewater treatment facility.
The city of Farmington regulates its emissions levels and works closely with the EPA to monitor, said Jeff Smaka, public works director.
The San Juan Watershed Group is working to identify sources of a second category of pollution, non-point sources.
Unfortunately, those can be difficult to identify, Tomko said.
Runoff from those fields can include fecal matter from grazing livestock and wildlife, he said.
"If a field is used for pasture then it ends up picking up bacteria that washes into the rivers," Tomko said.
Some simple solutions could be to shift to sprinkler irrigation systems and to fence cattle and other livestock out of fields, he said.
"Our goal is to try and improve water quality so that rivers are no longer listed (by the EPA)," Tomko said.
But the process has been difficult.
"We're in a political and jurisdictional mishmash," Tomko said.
The state of Colorado has its own EPA standards, he said. New Mexico and each tribal government in the region has a different set of standards.
Nevertheless, action is needed, Tomko said.
Ignoring water quality can have significant financial consequences for the tri-city area, he said. Because of new EPA regulations, the city of Aztec had to upgrade its wastewater treatment facility, and upgrades can cost hundreds of thousands of dollars.
The San Juan Watershed Group and the Animas Watershed Partnership, however, are not regulatory organizations, Tomko said. The groups hope work with willing property owners to find solutions that maintain property integrity while improving the river ecosystem.
The organizations have been trying to spread the word about grants available to work with landowners to improve properties, he said.
One of those grants include $500,000 from BHP Billiton awarded to the San Juan Watershed Group after a $10 million settlement in March 2012 between the international company, PNM Resources and the Sierra Club.