Asked whether people might one day go for a swim in Chicago’s Little Calumet River, environmental advocate Tom Shepherd snorted.

“When I was a kid we used to jump in there,” he said. “And we didn’t know anything about what kind of dangers were lurking in there but we did nevertheless, and we came out all black and grimy.”

Shepherd, who works with the Southeast Environmental Task Force, now knows as well as anyone that the Calumet waterways have been severely polluted for over a century by a potent mix of toxic run-off from steel mills and sewage from the Metropolitan Water Reclamation District (MWRD) of the greater Chicago area. To this day, water flows from MWRD plants into the river without being disinfected to federal standards. An innocent kayaker who splashes water in her own face may be hit with a faceful of fecal bacteria.

“We have been advocating for disinfection for a long time,” Shepherd said.

That disinfecting treatment is finally in sight. Illinois Governor Pat Quinn announced Monday that the state is giving $250 million in loans to the MWRD to help clean up Chicago-area waterways and replace aging infrastructure. More than half of the money will go to build facilities at the Calumet and O’Brien treatment plants that take dangerous bacteria out of wastewater before it hits the Chicago or Calumet Rivers. Some of the funded projects will also help keep sewers from overflowing, which sends raw sewage into the waterways with relative frequency.

Quinn also touted the creation of 2,000 unionized jobs with the low-interest loans, which are a part of the Illinois Clean Water Initiative.

The shift towards cleaner rivers hasn’t come easy. For years the publicly-elected MWRD commission fought for the right to not clean up Chicago’s waterways. After a prolonged legal struggle, in 2011 the MWRD announced it had reached an agreement with the U.S. Environmental Protection Agency to start better managing polluted storm runoff and enforcing EPA standards for water it releases from its plants. At that time the Chicago Tribune reported that between 60 and 100 percent of the water in the Chicago River on a given day originated in a wastewater treatment plant and came out only partially treated. The numbers in the Little Calumet, Chicago’s branch of the Calumet River, are similar.

Shepherd said he doesn’t see swimmers getting in the Little Calumet any time soon, but boaters are already coming back.

“It’s pretty exciting. This summer we’re doing more paddling on the river, we’re bringing recreation, we have a great trail that’s being developed,” he said.

With Governor Quinn’s support, in 2011 the Southeast Environmental Task Force was involved with declaring a large area of heavily polluted wetlands near Lake Calumet a future wildlife reserve. At a press conference Monday, Quinn referenced the positive effects the water clean-up will have on that project, called the Millenium Reserve.

“You have eagles who actually live here. How many urban areas in the whole United States have eagles?” Quinn said. “It’ll be the largest conservation area in any urban environment in the whole United States, but in order to make it worthwhile, you’ve gotta have clean water.”

Shepherd, who has seen the eagles nesting in the south side wetlands, was hopeful about the clean-up efforts, but a little more reserved than Quinn.

“Someday we may be able to fish out there,” he said.