Updated August 2026
Cleanest Lakes in Minnesota: Top 25 Ranked by Water Quality
Filtered to remove lakes with limited data (<3 sampling years). Sorted by overall water quality score.
The single cleanest lake in Minnesota is Rainy Lake, with the highest combined water quality score in our 2026 dataset (grade A). Cleanliness is measured by Secchi depth (clarity), total phosphorus, and chlorophyll-a — all sourced from EPA Water Quality Portal and state agency sampling. The full top 25 ranked list appears below.
The "cleanest" ranking on LakeGrade is composite: water clarity (Secchi), total phosphorus, and chlorophyll-a — the three core inputs to the LakeGrade rubric — taken together. The cleanest Minnesota lake on the current data is Rainy Lake (A).
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 | Rainy Lake | Cass | A | 13.9 ft | 11.5 µg/L | 1.8 µg/L | 129 acres |
| 2 | Crane Lake | Otter Tail | A | 9 ft | 15 µg/L | 6.4 µg/L | 350 acres |
| 3 | Lobster Lake | Douglas | A | 13 ft | 20.5 µg/L | 3.6 µg/L | 1,334 acres |
| 4 | East Fox Lake | Crow Wing | A | 16.4 ft | 10 µg/L | 2.7 µg/L | 241 acres |
| 5 | Deep Portage Lake | Cass | A | 15.4 ft | 9 µg/L | 1.6 µg/L | 129 acres |
| 6 | Clearwater Lake | Cook | A | 29 ft | 4 µg/L | 1.3 µg/L | 462 acres |
| 7 | Clearwater Lake | Wright | A | 9.8 ft | 22 µg/L | 6.3 µg/L | 3,187 acres |
| 8 | Clearwater Lake | Clearwater | A | 10 ft | 16 µg/L | 3.2 µg/L | 999 acres |
| 9 | Lower Hay Lake | Crow Wing | A | 18.5 ft | 13 µg/L | 2.7 µg/L | 700 acres |
| 10 | Latoka Lake | Douglas | A | 19 ft | 11 µg/L | 2.2 µg/L | 767 acres |
| 11 | Little Birch Lake | Todd | A | 13 ft | 19 µg/L | 3.1 µg/L | 839 acres |
| 12 | North Long Lake | Crow Wing | A | 15.1 ft | 14 µg/L | 2.7 µg/L | 6,190 acres |
| 13 | Bad Medicine Lake | Becker | A | 25 ft | 6 µg/L | 1.6 µg/L | 803 acres |
| 14 | Mud Lake | Becker | A | 12.5 ft | 22 µg/L | 5.9 µg/L | 1,178 acres |
| 15 | Big Lake | Beltrami | A | 9.7 ft | 15 µg/L | 4.8 µg/L | 3,598 acres |
| 16 | Big Lake | Carlton | A | 10 ft | 13.5 µg/L | 3.2 µg/L | 526 acres |
| 17 | Big Lake | Sherburne | A | 13.6 ft | 10.5 µg/L | 6.1 µg/L | 254 acres |
| 18 | Big Sugar Bush Lake | Becker | A | 16.5 ft | 10 µg/L | 2.7 µg/L | 522 acres |
| 19 | Pelican Lake | Otter Tail | A | 16.4 ft | 15 µg/L | 3 µg/L | 3,962 acres |
| 20 | Pelican Lake | Crow Wing | A | 14.3 ft | 11 µg/L | 2.7 µg/L | 8,367 acres |
| 21 | Fullers Lake: East Basin | Beltrami | A | 15 ft | 10 µg/L | 2.4 µg/L | - |
| 22 | Birch Lake | Ramsey | A | 5.9 ft | 21 µg/L | 3.3 µg/L | - |
| 23 | Birch Lake | Wright | A | 15 ft | 17 µg/L | 4 µg/L | 100 acres |
| 24 | Birch Lake | Cass | A | 14 ft | 12 µg/L | 4 µg/L | 1,267 acres |
| 25 | Round Lake | Aitkin | A | 14.5 ft | 10 µg/L | 2.7 µg/L | 737 acres |
Clearest lakes in Minnesota by water clarity
“Clearest” ranks by Secchi depth — how far you can see into the water — which can differ from the combined cleanliness score above. The clearest water in Minnesota is St James Pit Lake at 47.6 ft of Secchi visibility.
- 1. St James Pit Lake — 47.6 ft, St. Louis County
- 2. Caribou Lake — 31 ft, Itasca County
- 3. Hunter Lake — 31 ft, Cass County
- 4. Clearwater Lake — 29 ft, Cook County
- 5. Three Island Lake — 29 ft, Itasca County
Frequently Asked Questions
What is the cleanest lake in Minnesota?
Rainy Lake has the highest water quality score in our 2026 Minnesota 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 Minnesota?
Among monitored Minnesota lakes, East Arctic 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 Minnesota has the cleanest water?
Minnesota's clearest waters are concentrated in deeper, lower-nutrient glacial basins with forested or low-agriculture watersheds. Among the current top-ranked lakes above, counties like Crow Wing, Cass, and Becker produce the highest-scoring lakes.
What is the clearest lake in Minnesota?
St James Pit Lake is the clearest lake in Minnesota by water clarity, with a Secchi depth of 47.6 feet — the deepest transparency in our 2026 dataset. "Clearest" ranks by Secchi depth (how far you can see into the water) specifically, while "cleanest" combines clarity with phosphorus and chlorophyll-a. See our full clearest-lakes ranking for Minnesota for the top 25 by Secchi clarity.
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 Minnesota 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 Minnesota, 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 Minnesota state norms and combined into a single 0–100 score. The lakes above are sorted by that combined score.Full methodology →
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Source: EPA National Aquatic Resource Surveys, 2026.