An environmental group’s challenge to Boise’s new wastewater discharge permits is complicating a pollution-trading proposal that federal regulators and Idaho leaders hope will help other U.S. cities manage sewage and reduce farming’s impact on water quality.

Idaho Rivers United objects to a new Environmental Protection Agency permit that limits phosphorous discharges from Boise’s two wastewater treatment plants into the Boise River only between May and September. The group wants limits to apply from October to April, too.

But Boise officials say the group’s demands could jeopardize the city’s plan to invest some $6 million in a plant to treat agricultural runoff 34 miles downstream on the Boise River, to generate “pollution offsets” to help it meet the EPA’s new summer limits.

The downstream project, called the Dixie Drain, may not generate offsets in winter months, when there’s less agricultural water to treat, forcing Boise to find another alternative.

Neal Oldemeyer, Boise public works director, declined May 2 to name the cost but has said improvements to the city’s existing wastewater treatment plants would run in the tens of millions — a cost that would be absorbed by city residents.

“It would be more difficult to make it work,” Oldemeyer told The Associated Press. “Our goal is, we would love to see Dixie go forward.”

Boise and other Idaho cities are under the gun to meet new EPA limits on their wastewater treatment plants’ phosphorous discharges that eventually end up in the Brownlee Reservoir on the Snake River, a polluted slackwater where algae blooms contribute to fish die-offs behind Idaho Power Co.’s Hell’s Canyon Dam complex.

Boise’s two treatment plants now pump out 1,100 pounds of phosphorus daily, under a previous EPA permit with no limits for phosphorous, mercury or ammonia.

To meet new EPA limits, Boise’s strategy is twofold: make improvements to the two treatment plants to cut phosphorous releases to less than 15 pounds per day; and use offsets from building the small treatment plant at the 97-year-old Dixie Drain, where water used to irrigate southwestern Idaho crops collects before entering the Boise River.

Irrigation return flows like at Dixie Drain aren’t required to limit phosphorous under the federal Clean Water Act, though the EPA lists farming as a leading polluter.

Regional EPA officials in Seattle declined to comment, citing Idaho Rivers United’s appeal.

But it’s clear the pollution-trading proposal at Dixie Drain is high on the agenda, not only for the federal agency but for Idaho’s leaders in Congress.

In 2010 the EPA’s top regional administrator, Dennis McLerran, toured the site between Parma and Notus, giving the project what amounted to an initial blessing. McLerran was accompanied by Idaho Republican Sen. Jim Risch, who called Boise’s aspirations an “innovative, first-of-its-kind approach.”

Boise also is eager because it’s already spent $500,000 to buy 49 acres at the site.

Idaho Rivers United said it doesn’t want to block the project, because it likes the idea of treating agricultural pollution.

“If Dixie Drain works as intended, I’d like to see a project like it at every agricultural drain in the valley,” said Kevin Lewis, an Idaho Rivers United activist.

Still, his group said in its appeal of the EPA phosphorous limits for Boise that it makes no sense to curb phosphorous discharges between May and September, while having no limits the rest of the year.

Though phosphorous contributes to Brownlee’s oxygen-sapping algae blooms primarily during the hot summer months, they’re increasingly observed at other times as the climate changes, Idaho Rivers United wrote. Phosphorous releases between October and April also pile up in sediment on the reservoir floor, contributing to future blooms.

One alternative: The EPA could establish winter limits for Boise high enough for the city to avoid expensive plant upgrades — and stay on track at Dixie Drain.

“We think there are solutions that will work for the city, work for Idaho Rivers United and work for the Boise River,” Lewis said.