One measure of a lakes health is the trophic state, which relates to the amount of algae in the water. The average summer trophic state for the last 5 years was 69 (Eutrophic) and was determined using chlorophyll data. For a Impounded Flowing Water lake, this is considered Fair.
Lake Wisconsin has been monitored by volunteers since 1993. Volunteers monitor water clarity with a black and white Secchi disk. Some also collect water samples, which are sent to the State Lab of Hygiene to be analyzed. Volunteers are the source of the majority of Wisconsin's lake water quality data, and their dedication is greatly appreciated. Additional monitoring has been done through projects funded in part by DNR Lake Grants and Aquatic Invasive Species Grants. Reports and graphs featuring data collected by volunteers, DNR staff and others can be viewed below.
| Station Name | Station ID | Map | Max Year | Reports |
|---|
| Lake Wisconsin (Merrimac) - Deep Hole | 573125 | Map | 2023 | Details |
| Lake Wisconsin - Gruber'S Grove Bay G03a | 10017166 | Map | 2007 | Details |
| Lake Wisconsin - Gruber'S Grove Bay G07b | 10017167 | Map | 2007 | Details |
| Lake Wisconsin - Gruber'S Grove Bay G11c | 10017168 | Map | 2007 | Details |
| Lake Wisconsin - Gruber'S Grove Bay G15a | 10017169 | Map | 2007 | Details |
| Lake Wisconsin - Gruber'S Grove Bay G19c | 10017170 | Map | 2007 | Details |
| Lake Wisconsin - Gruber'S Grove Bay G23a | 10017171 | Map | 2007 | Details |
| Lake Wisconsin - Gruber'S Grove Bay G27b | 10017172 | Map | 2007 | Details |
| Lake Wisconsin - Gruber'S Grove Bay G31b | 10017173 | Map | 2007 | Details |
| Lake Wisconsin - Gruber'S Grove Bay G35c | 10017174 | Map | 2007 | Details |
| Lake Wisconsin - Harmony Grove Site F | 10041146 | Map | 2001 | Details |
| Lake Wisconsin - Just W Of Whalen Grade | 113077 | Map | 2022 | Details |
| Lake Wisconsin - Main Channel off Moon Valley | 10050871 | Map | 2023 | Details |
| Lake Wisconsin - Near Dam | 10028976 | Map | 2011 | Details |
| Lake Wisconsin - Okee Bridge | 10028900 | Map | 2023 | Details |
| Lake Wisconsin - SW of Weigand's Bay - Off Pier | 10042586 | Map | 2023 | Details |
| Lake Wisconsin - SW of Weigands Bay | 10031186 | Map | 2015 | Details |
| Lake Wisconsin - Sticky Bay - Center | 10029002 | Map | 2023 | Details |
| Lake Wisconsin - Wiegands Bay off Wiegands Bay North Rd | 10057991 | Map | 2023 | Details |
| Lake Wisconsin - betw. Stoners Bay and Pine Bluff | 10031184 | Map | 2022 | Details |
| Lake Wisconsin Columbia Co - Harmony Grove Site D | 10007590 | Map | 2009 | Details |
| Lake Wisconsin Columbia Co. - Harmony Grove Site A | 10007593 | Map | 2009 | Details |
| Lake Wisconsin Columbia Co. - Harmony Grove Site B | 10007592 | Map | 2012 | Details |
| Lake Wisconsin Columbia Co. - Harmony Grove Site C | 10007591 | Map | 2009 | Details |
| Lake Wisconsin Columbia Co. - Harmony Grove Site E | 10007589 | Map | 2011 | Details |
| Lake Wisconsin Columbia Co. - No Name Bay | 10007594 | Map | 2005 | Details |
| Lake Wisconsin Columbia Co. - Sunset Bay | 10007596 | Map | 2023 | Details |
| Lake Wisconsin Columbia Co. - Turtle Bay | 10007595 | Map | 2023 | Details |
| Lake Wisconsin Palisade Street Bay | 10042254 | Map | 2023 | Details |
| Lake Wisconsin Whalen's Grade | 10042253 | Map | 2022 | Details |
| Lake Wisconsin- Okee Bay South (Mouth of Spring Creek) | 10039885 | Map | 2013 | Details |
| Wisconsin River - Grubers Grove Bay Lake WIsconsin | 10029823 | Map | 2009 | Details |
| Wisconsin River - Grubers Grove Bay Lake Wisconsin | 10029820 | Map | 2009 | Details |
| Wisconsin River - Grubers Grove Bay Lake Wisconsin | 10029822 | Map | 2009 | Details |
| Wisconsin River - Grubers Grove Bay Lake Wisconsin | 10029821 | Map | 2009 | Details |
| Wisconsin River - Grubers Grove Wisconsin River #19 | 10029814 | Map | 2009 | Details |
| Wisconsin River - Grubers Grove Wisconsin River #21 | 10029815 | Map | 2009 | Details |
| Wisconsin River - Grubers Grove Wisconsin River #26 | 10029816 | Map | 2009 | Details |
| Wisconsin River - Grubers Grove Wisconsin River #33 | 10029817 | Map | 2009 | Details |
| Wisconsin River - Grubers Grove Wisconsin River #34 | 10029818 | Map | 2009 | Details |
| Wisconsin River - Grubers Grove Wisconsin River #36 | 10029819 | Map | 2009 | Details |
| Wisconsin River - Grubers Grove Wisconsin River #6 | 10029812 | Map | 2009 | Details |
| Wisconsin River - Grubers Grove Wisconsin River #9 | 10029813 | Map | 2009 | Details |
| Wisconsin River - Lake Wisconsin - Downstream of Merrimac RR Bridge | 115016 | Map | 2012 | Details |