Contaminant levels remain high, however.
The San Juan Watershed Group found E. Coli, phosphorus, excess nutrients, high water temperature and sediment along stretches of the San Juan River.
The group also found that sections of the Animas, La Plata and San Juan rivers have E. Coli concentrations ranging from 40-80 percent higher than the state environment department's threshold.
E. Coli is most often deposited into rivers through fecal matter in storm runoff, flood irrigation of grazed pastures, livestock wandering into streams and faulty or illegal septic tanks.
The Animas Watershed Partnership found that sections of the Animas River exceeded acceptable levels of manganese, E. Coli, phosphorus, sediment, water temperature, nutrients and turbidity — cloudiness caused by suspended particles.
Farmington City Council heard a joint presentation by both conservation groups Tuesday morning.
"The San Juan River and the Animas River are critical common resources," said Ann Oliver, of the Animas Watershed Partnership. "We want to talk to you about two groups that aren't regulatory in nature."
The pollution, it appears, could have an effect on city infrastructure.
Higher concentrations of fecal matter in the water supply could impact the city's water treatment costs, said Jeff Smaka, public works director.
"The higher the concentration, the longer the treatment time," Smaka said.
For the last few years, the groups have been working on a watershed plan, Oliver said.
The plan involves sampling to identifying pollution sources, tracking sources of bacteria, identifying best management practices to help farmers and ranchers reduce pollutant runoff and reaching out to the community for cooperation.
This community effort, Oliver said, will be critical in ensuring river health.
"Everything's floating downstream," she said. "We're tied together by the river. We're all about collaboration. We want to solve problems without conflict."
For more information on the San Juan Watershed Group, contact Julia Campus at firstname.lastname@example.org or call 505-334-3090 ext. 116.