Half of Minneapolis’ 12 public beaches remained shut down Wednesday due to high measurements of E. coli or reports of related illness, with the exceptionally rainy summer contributing to the city’s worst season for beach closures in years.

Two beaches at Lake Nokomis on Tuesday became the latest to be shut down after three children became sick while swimming. Though that number is small compared to the 116 people who reported falling ill after swimming at Lake Minnetonka’s Big Island during the July 4th weekend, the bacteria has nonetheless forced the city to empty some of its most popular beaches during the height of the swimming season.

This summer has brought the most beach closures at one time since the Minneapolis Park and Recreation Board began testing for the bacteria in 2003, said Debra Pilger, the Park Board’s director of environmental management. It is also the first time in her 25-year history with the Park Board that beaches have been closed because of illness reports, she said, rather than simply because of test results.

The number of beach closures is “unusually high,” Pilger said, spurred on by one of the wettest years ever for the metro area. Minneapolis has gotten 26.68 inches of rain this year — about 6.9 inches above average — making it the fifth-wettest to date in recorded history, according to the National Weather Service.

Stormwater runoff can wash fecal contamination and other bacteria sources, including animal waste, soil and anything else found on top of roofs, in yards and on the streets, directly into lakes.

“That’s just a fact in urban environments,” Pilger said. “All that stormwater runoff, all that rain, brings everything in off the streets, off the yards, off the beach itself.”

The illness reports led the State Health Department to reach out to people who recently held events at Lake Nokomis, including the YWCA Women’s Triathlon, which was held on Sunday. More than 1,500 people participated in the race, which starts with a swim in the lake.

A spokeswoman for YWCA Minneapolis said it hadn’t heard yet of any athletes becoming sick after the race. The organization encouraged athletes to take the State Department’s online survey if they were feeling symptoms, such as stomach cramps or diarrhea.

The state Health Department has received a “steady stream of calls” from people feeling that they could be sick, spokesman Doug Schultz said. However, there were no new confirmed cases of illness Wednesday, as it takes a longer time to evaluate individual reports, he said.

The Park Board tests the city’s lakes each Monday during the summer to make sure E. coli levels stay within state standards. Levels are usually elevated if it rained one or two days before testing, Pilger said.

In addition to runoff, other sources can also contribute to greater levels of bacteria, including droppings from geese and other waterfowl, sick swimmers or children with leaking diapers.

Some beaches, including the 32nd Street beach at Bde Maka Ska/Lake Calhoun, and Lake Hiawatha, have been closed since June, Pilger said. The two beaches at Lake Nokomis were the most recent to close as the Minnesota Department of Health investigates what led three children to become sick after swimming there.

Unlike the closures at Bde Maka Ska and Lake Hiawatha, the contamination of Lake Nokomis could be linked to a sick swimmer who entered the water, said Trisha Robinson, supervisor of the department’s waterborne diseases unit. The strain of bacteria detected — Shiga toxin-pro­duc­ing E. coli or STEC — is easily transferable, she said.

“When you enter an untreated body of water like a lake, you can spread it to other people who accidentally ingest the water,” Robinson said. “Just the small amount of fecal material that people bring into the water with them, that washes off into the water and … it can make us sick.”

Robinson said it could take up to a week after swimming for people to develop symptoms.

The Park Board has several educational programs to keep contaminants off lakes, and has wetland ponds that help collect more runoff from entering the water.

Pilger said that people should not come to the beach if they’re sick, adding that “everyone’s got a role in keeping the lake healthy and clean.”

As stronger rains and wetter winters are predicted in Minnesota in the coming years due to climate change, Pilger said, the Park Board needs to look beyond the city to find out how lakes are being affected.

“We need to get some time to look at what’s happening in other municipalities in the metro, what’s happening in the state, what’s happening in the Midwest,” she said. “Is this a phenomenon that’s happening elsewhere, too? Are other entities seeing more beach closings?”

Star Tribune writer Liz Sawyer contributed to this report.