Cleanest Lakes in Wisconsin
Main Section Lake ranks #1 for water quality in Wisconsin with a grade of A. Below: the top 25 cleanest lakes in Wisconsin by combined Secchi clarity, phosphorus, and chlorophyll-a from 2026 EPA + DNR sampling.
Filtered to remove lakes with limited data (<3 sampling years). Sorted by overall water quality score.
Ranking the cleanest New York lakes means picking the basins that score high on all three water-quality dimensions, not just one. Main Section Lake leads the list with a grade of A, with Queneska Island Lake close behind.
The top of the cleanest-lakes list is dominated by deep, glacial, cold-water basins — the same basins that produce the A-grade bracket overall. The pattern is not coincidence: depth and watershed land-use are the dominant inputs to water-clarity and nutrient-loading both.
| Rank | Lake | County | Grade | Clarity | Phosphorus | Chlorophyll-a | Area |
|---|---|---|---|---|---|---|---|
| 1 | Main Section Lake | Essex | A | 15.7 ft | 9.5 µg/L | 4.6 µg/L | - |
| 2 | Queneska Island Lake | Essex | A | 17.4 ft | 15 µg/L | 3.4 µg/L | - |
| 3 | Owasco Lake Platform | Cayuga | A | 11 ft | 6 µg/L | 2 µg/L | - |
| 4 | Seneca Lake Platform | Seneca | A | 11.5 ft | 6 µg/L | 2.6 µg/L | - |
| 5 | Isle la Motte Lake | Clinton | A | 15.4 ft | 8.7 µg/L | 5 µg/L | - |
| 6 | Isle la Motte Lake | Clinton | A | 12.5 ft | 12.3 µg/L | 4.6 µg/L | - |
| 7 | Main Section Lake | Clinton | A | 14.8 ft | 9.4 µg/L | 4.7 µg/L | - |
| 8 | Sodus Bay Lake | Wayne | B | 8 ft | 18 µg/L | 9.1 µg/L | - |
| 9 | Irondequoit Bay Lake | Monroe | C | 7 ft | 27.5 µg/L | 12.9 µg/L | - |
| 10 | Southern Section Lake | Essex | C | 2.6 ft | 22.9 µg/L | 10.4 µg/L | - |
| 11 | Southern Section Lake | Washington | D | 2 ft | 36.7 µg/L | 13.8 µg/L | - |
| 12 | Irondequoit Bay Lake | Monroe | D | 5.3 ft | — | 24.2 µg/L | - |
| 13 | Lk Ontario Lake | Monroe | D | — | 126 µg/L | 17.1 µg/L | - |
Frequently Asked Questions
What is the cleanest lake in Wisconsin?
Main Section Lake has the highest water quality score in our 2026 Wisconsin dataset (grade A), based on combined Secchi clarity, phosphorus, and chlorophyll-a measurements. Cleanliness here means low nutrient load, deep water clarity, and minimal algae — measured directly from EPA and state DNR samples.
What is the most polluted lake in Wisconsin?
Among monitored Wisconsin lakes, Lk Ontario Lake ranks among the most polluted by combined phosphorus and chlorophyll-a load. See our full ranking on the most-polluted-lakes trend page for state-by-state details.
Where in Wisconsin has the cleanest water?
Wisconsin's clearest waters are concentrated in the deeper, lower-nutrient lakes of the state's northeast — typically older glacial lakes with rocky basins and forested watersheds. The top 25 above shows the highest-scoring lakes statewide; counties like Cook, Lake, and Itasca (MN) or Vilas, Oneida, and Iron (WI) consistently produce A-grade waters.
Are these lakes safe to swim in?
A and B grade lakes are typically safe for swimming under normal conditions. Chlorophyll-a below 10 µg/L means low risk of harmful algal blooms. Always check posted advisories before swimming — water quality changes seasonally, especially in late summer when blue-green algae bloom risk peaks.
How are these grades calculated?
Each lake is scored on three signals: Secchi depth (water clarity in feet), total phosphorus (nutrient load in µg/L), and chlorophyll-a (algae concentration in µg/L). Each gets a 0–100 sub-score relative to Wisconsin state norms. The three sub-scores average into the overall score, which maps to an A–F letter grade. Methodology details live on our methodology page.
What are the top 5 cleanest lakes in the US?
There is no single national ranking of cleanest lakes — each state agency uses different metrics. Crater Lake (Oregon) is widely cited as the clearest US lake, with Secchi depths over 30 m. Lake Tahoe and Lake Superior are also top-tier nationally. Within Wisconsin, the lakes ranked above are the top 25 by our standardized 2026 grading.
How we rank cleanest lakes
Cleanliness here means three things working together:
- Secchi clarity — how deep you can see into the water (in feet). Greater depth = clearer water = lower suspended sediment and algae.
- Total phosphorus — the nutrient that fuels algae. Lower phosphorus levels mean less algae growth potential.
- Chlorophyll-a — the green pigment in algae. Direct measurement of how much algae is currently in the water.
Each signal is normalized against Wisconsin state norms and combined into a single 0–100 score. The lakes above are sorted by that combined score.Full methodology →
Source: EPA National Aquatic Resource Surveys, 2026.