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 57 (Eutrophic) and was determined using chlorophyll data. For a Reservoir lake, this is considered Good.
Minong Flowage has been monitored by volunteers since 1989. 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 |
|---|
| Minong Flowage - Center Large Bay | 10029932 | Map | 2009 | Details |
| Minong Flowage - Central Basin | 664041 | Map | 1979 | Details |
| Minong Flowage - Central Basin | 10031146 | Map | 2011 | Details |
| Minong Flowage - Channel from Cranberry | 10029933 | Map | 2009 | Details |
| Minong Flowage - Channel from North Basin | 10033625 | Map | 2011 | Details |
| Minong Flowage - County Boat Landing Bay | 10029939 | Map | 2009 | Details |
| Minong Flowage - County Park | 10029934 | Map | 2009 | Details |
| Minong Flowage - Cranberry Flowage at Hwy T | 10031147 | Map | 2010 | Details |
| Minong Flowage - Cranberry Flowage at Hwy T | 10029938 | Map | 2014 | Details |
| Minong Flowage - Deep Hole 1/3 Mi Above Dam | 663099 | Map | 2023 | Details |
| Minong Flowage - East Shore Bed | 10031145 | Map | 2011 | Details |
| Minong Flowage - Near County Park | 10031144 | Map | 2010 | Details |
| Minong Flowage - Near County Park Beach | 10031143 | Map | 2011 | Details |
| Minong Flowage - Near South Island | 10033628 | Map | 2011 | Details |
| Minong Flowage - Near WR NW Basin | 10029931 | Map | 2009 | Details |
| Minong Flowage - Near WR Two | 10029936 | Map | 2009 | Details |
| Minong Flowage - Near Youth Camp | 10029941 | Map | 2011 | Details |
| Minong Flowage - North Basin | 10029924 | Map | 2021 | Details |
| Minong Flowage - North Basin | 10031140 | Map | 2011 | Details |
| Minong Flowage - North Part of North Basin | 10033623 | Map | 2011 | Details |
| Minong Flowage - North of County Line | 10033627 | Map | 2011 | Details |
| Minong Flowage - SW Bay of North Basin | 10033624 | Map | 2011 | Details |
| Minong Flowage - Serenity Bay | 10031141 | Map | 2014 | Details |
| Minong Flowage - Serenity Bay North | 10031153 | Map | 2011 | Details |
| Minong Flowage - Serenity Bay S of Zizania | 10033620 | Map | 2011 | Details |
| Minong Flowage - Serenity Bay SE of Zizania | 10033619 | Map | 2011 | Details |
| Minong Flowage - Serenity Bay W of Zizania | 10033621 | Map | 2011 | Details |
| Minong Flowage - Serenity Bay West | 10033622 | Map | 2011 | Details |
| Minong Flowage - Shallows North of County Park | 10033629 | Map | 2011 | Details |
| Minong Flowage - Site A-Central Basin - NW Of Youth Camp | 163300 | Map | 2023 | Details |
| Minong Flowage - Site B-Hwy T Bridge | 163247 | Map | 2011 | Details |
| Minong Flowage - South Central Bay | 10029935 | Map | 2009 | Details |
| Minong Flowage - W of Channel from North Basin | 10033626 | Map | 2011 | Details |
| Minong Flowage - Youth Camp | 10031142 | Map | 2010 | Details |
| Minong Flowage - near DNR Landing | 10029937 | Map | 2009 | Details |
| Minong Flowage -- Center Basin-Sand Island [Herbicide Monitoring Site CSI-16] | 10044902 | Map | 2016 | Details |
| Minong Flowage -- Center Basin-CountyBeach [Herbicide Monitoring Site OffCC-16] | 10044898 | Map | 2016 | Details |
| Minong Flowage -- DNR Bay [Herbicide Monitoring Site DBE-16] | 10044900 | Map | 2016 | Details |
| Minong Flowage -- DNR Bay [Herbicide Monitoring Site DBO-16] | 10044896 | Map | 2016 | Details |
| Minong Flowage -- DNR Bay [Herbicide Monitoring Site DBW-16] | 10044901 | Map | 2016 | Details |
| Minong Flowage -- Near Dam [Herbicide Monitoring Site NrD-16] | 10044899 | Map | 2016 | Details |
| Minong Flowage at Smith Bridge | 163246 | Map | 2000 | Details |
| Minong Flowage-Totagatic River - Near Dam | 663046 | Map | 1994 | Details |
| North Sand Island- Minong Flowage | 10055251 | Map | 2023 | Details |
| Sawdust Island- Minong Flowage | 10055249 | Map | 2023 | Details |
| Totogatic River at Serenity Bay | 10055250 | Map | 2022 | Details |