The Mississippi River headwaters and two Lake Superior beaches, along with hundreds of other lakes and river segments, have been added to the state’s list of waterways that are “impaired” due to pollutants or other problems that threaten fish, plant life or public health.

The additions, outlined in a report released Wednesday by the Minnesota Pollution Control Agency (MPCA), are part of federal environmental reporting requirements as well as a 10-year effort by the state to assess all 80 of its watersheds.

More than halfway complete, the inventory has found impairments in roughly 40 percent of the bodies of water that it has checked statewide.

“More than half of the waters are not impacted, and that’s good,” said Glenn Skuta, director of the MPCA’s watershed division. “But that’s still a pretty high percentage of waters that are not doing as well as they should be. It just points out the need for us to develop a better water ethic in Minnesota.”

Testing over the past two years found 582 new sources of pollution in 318 lakes, rivers and streams. That included 304 stream segments and nine lakes that can’t fully support fish and aquatic life, plus 87 bodies of water with high levels of phosphorus, which can breed algae and disrupt the oxygen levels needed for healthy plants and fish.

Tests found elevated mercury levels in fish in the section of the Mississippi extending north and east from the headwaters to Cass Lake in Beltrami County. Primarily a product of coal-burning power plants worldwide, excessive mercury can contaminate fish, which can then present health risks if they are caught and eaten, Skuta said.

The state typically issues fish consumption advisories for such contaminated waterways. Excessive mercury consumption is particularly bad for pregnant women due to the known link to birth defects.

With the new listings, the state now knows of 4,600 lakes, streams or segments of rivers that are considered impaired.

Mercury is the leading contaminant, accounting for one-third of the listings.

Nutrient imbalances such as excessive phosphorus are the second most common problem, resulting for example in a new impairment designation for the section of the Blue Earth River stretching south from the Rapidan Dam.

Farm fertilizers and drainage practices have been linked to algae blooms and damaging changes in such waterways. The state Department of Agriculture created a program that gives farmers incentives to use conservation practices; the program has certified 204 farms and kept thousands of pounds of sediment and phosphorus out of waterways, said Brad Redlin, the program’s manager.

Stretches of Minneopa Creek between New Ulm and Mankato also made the impaired list due to declines in the health of its fish population, while the Park Point beach in Duluth and the Agate Bay beach in Two Harbors were added because of potentially harmful levels of E. coli bacteria.

Both beaches are on calmer sections of Lake Superior protected by inlets; the Minnesota Department of Health recently issued a “no water contact” recommendation at the Agate beach due to the E. coli testing.

This year’s report also found some success stories. Cleanup efforts resulted in the “delisting” of two lakes — Red Rock Lake in Eden Prairie and Shaokotan Lake near the South Dakota border. Community leaders in southwest Lincoln County have been working since the 1990s to reduce manure runoff and problems with failing septic tanks that had resulted in problematic phosphorus levels in that lake, Skuta said.

Ironically, some residents around the Eden Prairie lake are disappointed with the delisting, which they believe will curtail the relatively modest water quality efforts.

Herbicides have helped contain weeds and improve the lake’s clarity and usability a bit, but there has been little to no effort to filter or manage the stormwater flowing into the suburban lake, said Mark David of the Friends of Red Rock Lake advocacy group.

“Its been better,” he said. “I don’t want to say it’s not better right now. The question is, what will it be like next year? [This] lake was forgotten about for so many years. We feel a little cheated.”

Public meetings to discuss the designations are being scheduled in coming weeks.

Among the state’s impaired waterways, roughly 1,900 have federally designated “Total Maximum Daily Load” plans to cut contaminants to acceptable levels. Most of the impaired waterways, however, do not yet have such plans.

Skuta said the agency’s current philosophy, given limited financial resources, is to target lakes or rivers that are close to the thresholds for contamination — on the theory that success is much more likely. However, he noted that bodies of water with extreme contamination can still be saved.

The environmental damage to the lake in Powderhorn Park in Minneapolis was once thought irreparable, but city and community efforts resulted in a successful cleanup. The lake was removed from the state impairment list in 2012 — a decade after it was first added.

“We don’t ever want to write off a lake or stream completely,” Skuta said. “Sometimes, we get surprised.”