Big Muskego Lake was monitored by volunteers between 1991 and 1998. Volunteers monitor water clarity with a black and white Secchi disk. 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 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 |
|---|
| Big Muskego Lake - Boxhorn's Launch [Herbicide Monitoring Site C16] | 10045051 | Map | 2016 | Details |
| Big Muskego Lake - Boxhorn's Launch [Herbicide Monitoring Site C17] | 10045049 | Map | 2016 | Details |
| Big Muskego Lake - Boxhorn's Launch [Herbicide Monitoring Site C22] | 10045052 | Map | 2016 | Details |
| Big Muskego Lake - Boxhorn's Launch [Herbicide Monitoring Site C23] | 10045050 | Map | 2016 | Details |
| Big Muskego Lake - Boxhorn's Launch [Herbicide Monitoring Site C29] | 10045053 | Map | 2016 | Details |
| Big Muskego Lake - Deep Hole | 683354 | Map | 2003 | Details |
| Big Muskego Lake - Durham Launch [Herbicide Monitoring Site B2] | 10045044 | Map | 2016 | Details |
| Big Muskego Lake - Durham Launch [Herbicide Monitoring Site B3] | 10045045 | Map | 2023 | Details |
| Big Muskego Lake - Durham Launch [Herbicide Monitoring Site B4] | 10045046 | Map | 2016 | Details |
| Big Muskego Lake - Durham Launch [Herbicide Monitoring Site B5] | 10045047 | Map | 2016 | Details |
| Big Muskego Lake - Durham Launch [Herbicide Monitoring Site B6] | 10045048 | Map | 2016 | Details |
| Big Muskego Lake - Hunter's Nest [Herbicide Monitoring Site A2] | 10045039 | Map | 2016 | Details |
| Big Muskego Lake - Hunter's Nest [Herbicide Monitoring Site A3] | 10045040 | Map | 2016 | Details |
| Big Muskego Lake - Hunter's Nest [Herbicide Monitoring Site A5] | 10045041 | Map | 2016 | Details |
| Big Muskego Lake - Hunter's Nest [Herbicide Monitoring Site A6] | 10045042 | Map | 2016 | Details |
| Big Muskego Lake - Hunter's Nest [Herbicide Monitoring Site A7] | 10045043 | Map | 2016 | Details |
| Big Muskego Lake - Limno No1 | 683346 | Map | 1994 | Details |
| Big Muskego Lake - Limno No2 | 683347 | Map | 1994 | Details |
| Big Muskego Lake - Limno No3 | 683348 | Map | 1994 | Details |
| Big Muskego Lake - Limno No4 | 683349 | Map | 1994 | Details |
| Big Muskego Lake - Limno No5 | 683350 | Map | 1994 | Details |
| Big Muskego Lake - Limno No6 | 683351 | Map | 1994 | Details |
| Big Muskego Lake - Limno No7 | 683352 | Map | 1994 | Details |
| Big Muskego Lake - Limno No8 | 683353 | Map | 1994 | Details |
| Big Muskego Lake - Sediment Core 01 Ne Corner Of Lake Basin | 683355 | Map | 1994 | Details |
| Big Muskego Lake - Sediment Core 05 Center E Of Large Island | 683359 | Map | 1994 | Details |
| Big Muskego Lake - Sediment Core 06 Wc Limno Area | 683360 | Map | 1994 | Details |
| Big Muskego Lake - Sediment Core 09 Se Heinrich'S- E Of Tern Island | 683363 | Map | 1994 | Details |
| Big Muskego Lake - Sediment Core 10 Sw Corner Of Lake Basin | 683364 | Map | 1994 | Details |
| Big Muskego Lake - South Site | 683309 | Map | 2002 | Details |
| Muskego (Big Muskego) Lake - Outlet Near Wind Lake | 643555 | Map | 2022 | Details |
| SW Outbranch of Big Muskego Lake near 5577228 | 10050788 | Map | 2010 | Details |