The rains that recently pummeled the state have continued to haunt east central Minnesota, in the form of a rising Mississippi River, flooding lakes and possibly widespread contamination.

State health officials on Friday warned Minnesotans heading to lakes in heavily flooded areas to avoid contact with floodwater, which may be contaminated by flooded septic systems. That would include swimming in or swallowing the water.

In Aitkin County, flood information officer Lynn Sue Mizner said it is likely that all 400 lakes have been contaminated and should be off-limits to swimmers. The state Health Department's alert does not apply to Lake Superior or beaches outside the Duluth harbor.

Aitkin County has been particularly hard-hit by high water, which has closed roads, contaminated wells and prompted residents around Big Sandy Lake to sandbag homes, and face the prospect of a cleanup and fix-up that could last into August. The lake's July 4th fireworks show on Floe Island has been canceled to keep the usual crowd of boats off the water.

Meanwhile, countless lakeshore owners across the region have been trying to figure out where their dock and boatlift parts have floated, how high they need to raise what's left, or when to reinstall a dock they've removed and raised several times already this season.

The Aitkin area got more than 12 inches of rain this month, pushing the Mississippi to a crest Wednesday higher than any since 1950. Big Sandy Lake, a reservoir of the river and popular recreation area surrounded by resorts, cabins and year-round homes, crested Thursday, also higher than it's been in more than 60 years.

At that point, the lake had risen 5.3 feet, contained nearly twice as much water and had 6.5 more square miles of surface area than it did only eight days before.

The Mississippi, which is so high that it is blocking water from draining out of Big Sandy Lake, is expected to drop only about a foot by late next week, with the lake slowly following. The Aitkin County Fair, scheduled for July 11-14, already has been canceled because of wet grounds.

A church near McGregor, Minn., has been set up as a meeting center and distribution site for water, food and cleaning supplies, while several residents have been placed in motels as temporary shelters, said Aitkin County Sheriff Scott Turner.

Bruce Johnson, a board member of the Big Sandy Lake Association who has owned a cabin on the lake for 25 years, said he and his wife, Virginia, won't be going up for the 4th as they usually do. "There's not really very much to do, and we can't really invite anybody there."

Plenty of challenges

The flood has brought a tide of issues to area residents, Johnson said.

Those include waterborne chemicals and organic matter from the river, as well as from overwhelmed septic systems, lawns and fire pits.

Submerged boat and dock equipment is another problem. Also, in many cases, water raised boats off their lifts into the canopies above them, before tearing everything away. "There's so much debris in the lake, I don't think people even know what they've lost yet," Johnson said.

Turner said flooded roads and no-wake zones are likely to be continuing problems for weeks.

The water in the Aitkin area will work its way down the Mississippi, but no serious flooding is expected because the river channel downstream and in the metro area is so much wider than it is up north, said Diane Cooper, hydrologist with the North Central River Forecast Center, a Chanhassen-based NOAA agency.

In the Brainerd Lakes area, 50 of the DNR's 130 docks were under water in recent days, and some boat ramps and lake access roads were washed out. The DNR has been scrambling to remove or raise those flooded docks and repair the ramps and access roads.

"We hope to have most of those docks pulled out by this weekend or by the 4th of July," said Wade Miller, DNR Parks and Trails area supervisor in Brainerd.

Four boat accesses have been closed, and DNR workers won't even check the status of state docks on the Mississippi until dangerous water levels recede.

Water-logged lakes

Lakes in Cass, Crow Wing and Aitkin counties nearly all have high water, Miller said, ranging up to 4 to 6 feet above normal. In some areas, pumps have been used to try to reduce water levels.

Brainerd-area dock installer Matt Lottman said he's been installing, removing, refiguring and reinstalling docks several times each on Gull Lake and the Whitefish chain. He usually knocks off in early June; this year, he has been employing a full crew and working seven days a week since March 24. Water is high enough that some docks still in the water may be destroyed if winds pick up, Lottman said.

The DNR's Miller urged boaters to use caution, both when launching boats and when motoring on the water. Sunken public and private docks and swimming platforms pose a serious risk, he said.

"We're also urging people to have respect for lakeshore owners on lakes with high water,'' he said, by slowing down and not creating wakes that cause shoreline erosion or even cabin flooding. Some lake associations also are urging boaters to slow down to prevent lakeshore erosion from waves.

Even as far north as the Boundary Waters, high water has forced at least one canoe outfitter at the end of the Gunflint Trail to install a temporary bricks-and-boards dock atop a submerged earthen dock. Wilderness Canoe Base office manager Katie Everett added, though, that with some portages under water, paddlers are finding they can paddle between some lakes without having to unload and carry canoes.

Greg Kruse, water monitoring unit supervisor for the DNR, noted that shallow lakes have seen significant expansion of water across shorelines and in some cases wetland areas. That could restore nutrients and habitat in those areas, he said.

Fewer problems in metro

High water has not created serious problems in the Twin Cities metro area. Lake Minnetonka, which had been reduced by drought since last summer, is now "about normal," said Telly Mamayek, spokeswoman for the Minnehaha Creek Watershed District, which monitors the lake as well. White Bear Lake, which hit a historic low in 2010, has risen about a foot this spring but is still more than 4 feet below its ordinary high water level.

Staff writer Doug Smith contributed to this story. Bill McAuliffe • 612-673-7646