The San Juan Watershed Group received a $500,000 grant as part of a lawsuit settlement to complete the project.
Funds for the project stem from a lawsuit the Sierre Club filed against BHP Billiton and Public Service Company of New Mexico.
The environmental groups alleged pollution from the businesses was entering nearby water.
The energy companies disputed the allegation but still settled the lawsuit in March for $10.2 million.
Much of the settlement money was allocated for environmental improvement projects, said David Tomko, the coordinator of the San Juan Watershed Group.
The watershed group will gather samples from the Animas River in Colorado near the state line, at Boyd Park and the Miller Street bridge in Farmington, Tomko said.
The group also will take samples from the San Juan River near the confluence of the Animas River and near Hogback, he said.
The samples will be taken weekly in from June through October and sent to a laboratory in Florida for study.
Tomko said in the last 10 years, sections of local rivers have exceeded New Mexico standards for the maximum amount of E. coli, a common bacteria that can cause serious infection in humans if people come into contact with harmful strains.
It is found in human and animal waste.
It's tough to answer what effect the E. coli levels have on
"The only real answer is that you have a greater risk of getting sick if you drink the river water," he said.
The E. coli levels could come from livestock, humans by means of faulty septic systems or from natural wildlife like deer and waterfowl, Tomko said.
The New Mexico Environment Department issued a list of New Mexico impaired rivers in Dec. 2011 that listed a 20-mile section of the Animas River beginning northeast of Aztec as a "category 5B" impairment, which means a review of river use policies is needed, according to environment department records.
If watershed group can determine the cause of local water pollution, it can lobby local governments for land-use policies that may help reduce E. coli levels, Tomko said.
Actual testing of the rivers is expected to last from September of this year to August 2014, he said. The group said it will receive ongoing updates on the water quality tests.
"Almost everyone can agree that bacteria loading is an important issue," Melissa May, who works with the watershed group and will be taking samples, said in a release. "It's a big year for the (San Juan Watershed Group). I think we'll be able to make real strides toward improving the water quality of the Animas."