From the DNR:

EAU CLAIRE, Wis. - Floods along Wisconsin rivers and streams can pose a potential health danger for private well users if wells are flooded. Well owners whose wells become flooded need to have the well tested before resuming use of the water, emphasized Department of Natural Resources water supply staff serving southwest Wisconsin.
That’s because floodwaters can contain bacteria and waste contaminants that threaten water supplies. Wells located in pits and basements are especially susceptible to such contamination.

“Any water supply system which as been overtopped by flood waters should be thoroughly disinfected and then tested to determine water safety,” said William Rogers, a DNR water supply specialist based at Eau Claire.

This work is best performed by licensed well drillers or pump installers. Wells should be disinfected with a strong chlorine solution or chlorine tablets. The chlorine must come into direct contact with all interior surfaces of the well, from top to bottom and throughout the distribution plumbing. The solution should remain in the system for 24 hours and then flushed from the system. Then a water sample can be collected and submitted for bacteriological testing, according to Mr. Roberts.

Information about how to chlorinate your well is available from DNR customer service centers in Fitchburg, Dodgeville, Horicon, La Crosse, Eau Claire, Wisconsin Rapids and Wausau or the DNR website at http://dnr.wi.gov/org/water/dwg/flood.htm

Water sampling kits are available from the State Laboratory of Hygiene at 1-800-442-4618. County health departments may also have sample bottles. You may contact the Crawford County Public Health Department at 608- 326-0229, the Richland Department of Health and Human Services at 608-647-8821 or the Vernon County Health Department at 608-637-5251.