Updated August 2026
Cleanest Lakes in Minnesota: Top 25 Ranked by Water Quality
Ranked from the Minnesota lakes with enough nutrient and algae sampling to compare. Lakes with fewer than three sampling years, and lakes nobody has sampled, are not ranked here.
The single cleanest lake in Minnesota is Rainy Lake (Cass County, MN), ranked first on its measured clarity and nutrients in the 2026 sampling record. Cleanliness here is measured by Secchi depth (clarity), total phosphorus, and chlorophyll-a — all sourced from EPA Water Quality Portal and state agency sampling, shown as reported. The full top 25 ranked list appears below.
Looking for the famous border lake? This #1 is the 129-acre Rainy Lake in Cass County. The much larger Rainy Lake on the Minnesota–Ontario border is a different lake — open Rainy Lake (Koochiching County, MN).
The "cleanest" ranking on LakeQuality is built from the measured nutrients and algae — phosphorus and chlorophyll-a read against EPA National Lakes Assessment 2022 ecoregion classes. Secchi clarity is shown and used only as a tiebreak. The cleanest Minnesota lake on the current data is Rainy Lake (Cass County, MN).
Many of Minnesota's highly ranked lakes are deep, glacial, cold-water basins. This list's #1 is different: the 129-acre Rainy Lake in Cass County.
| Rank | Lake | County | Clarity | Phosphorus | Chlorophyll-a | Area |
|---|---|---|---|---|---|---|
| 1 | Rainy Lake (Cass County, MN) | Cass | 13.9 ft | 11.5 µg/L | 1.8 µg/L | 129 acres |
| 2 | Crane Lake | Otter Tail | 9 ft | 15 µg/L | 6.4 µg/L | 350 acres |
| 3 | Lobster Lake | Douglas | 13 ft | 20.5 µg/L | 3.6 µg/L | 1,334 acres |
| 4 | East Fox Lake | Crow Wing | 16.4 ft | 10 µg/L | 2.7 µg/L | 241 acres |
| 5 | Deep Portage Lake | Cass | 15.4 ft | 9 µg/L | 1.6 µg/L | 129 acres |
| 6 | Clearwater Lake | Cook | 29 ft | 4 µg/L | 1.3 µg/L | 462 acres |
| 7 | Clearwater Lake | Wright | 9.8 ft | 22 µg/L | 6.3 µg/L | 3,187 acres |
| 8 | Clearwater Lake | Clearwater | 10 ft | 16 µg/L | 3.2 µg/L | 999 acres |
| 9 | Lower Hay Lake | Crow Wing | 18.5 ft | 13 µg/L | 2.7 µg/L | 700 acres |
| 10 | Latoka Lake | Douglas | 19 ft | 11 µg/L | 2.2 µg/L | 767 acres |
| 11 | Little Birch Lake | Todd | 13 ft | 19 µg/L | 3.1 µg/L | 839 acres |
| 12 | North Long Lake | Crow Wing | 15.1 ft | 14 µg/L | 2.7 µg/L | 6,190 acres |
| 13 | Bad Medicine Lake | Becker | 25 ft | 6 µg/L | 1.6 µg/L | 803 acres |
| 14 | Mud Lake | Becker | 12.5 ft | 22 µg/L | 5.9 µg/L | 1,178 acres |
| 15 | Big Lake | Beltrami | 9.7 ft | 15 µg/L | 4.8 µg/L | 3,598 acres |
| 16 | Big Lake | Carlton | 10 ft | 13.5 µg/L | 3.2 µg/L | 526 acres |
| 17 | Big Lake | Sherburne | 13.6 ft | 10.5 µg/L | 6.1 µg/L | 254 acres |
| 18 | Big Sugar Bush Lake | Becker | 16.5 ft | 10 µg/L | 2.7 µg/L | 522 acres |
| 19 | Pelican Lake | Otter Tail | 16.4 ft | 15 µg/L | 3 µg/L | 3,962 acres |
| 20 | Pelican Lake | Crow Wing | 14.3 ft | 11 µg/L | 2.7 µg/L | 8,367 acres |
| 21 | Fullers Lake | Beltrami | 15 ft | 10 µg/L | 2.4 µg/L | - |
| 22 | Birch Lake | Ramsey | 5.9 ft | 21 µg/L | 3.3 µg/L | - |
| 23 | Birch Lake | Wright | 15 ft | 17 µg/L | 4 µg/L | 100 acres |
| 24 | Birch Lake | Cass | 14 ft | 12 µg/L | 4 µg/L | 1,267 acres |
| 25 | Round Lake | Aitkin | 14.5 ft | 10 µg/L | 2.7 µg/L | 737 acres |
Get updates when Minnesota's cleanest-lake list changes
New nutrient and algae samples can move a lake up or down this ranking. Unsubscribe anytime.
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
Planning a winter trip? See ice-fishing lakes in Minnesota
The ranking above is about water quality, not ice. For hard-water season, start with best ice fishing lakes in Minnesota and ice fishing in Minnesota. LakeQuality does not measure ice thickness; check local ice reports before you go.
Frequently Asked Questions
What is the cleanest lake in Minnesota?
Rainy Lake (Cass County, MN) ranks first on measured clarity and nutrients in the 2026 Minnesota sampling record. Each lake's nutrient and algae readings — total phosphorus, total nitrogen, chlorophyll-a, and turbidity — are shown beside the EPA National Lakes Assessment 2022 condition class for that lake's own ecoregion, so a reading is compared against the lakes it would naturally resemble. LakeQuality publishes no letter grade. Cleanliness here means a low nutrient load and little algae, measured directly from EPA and state DNR samples; where two lakes tie on nutrients and algae, the deeper Secchi reading ranks first.
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?
Not on the readings alone. Clarity and nutrient readings are not a swimming clearance — it does not measure E. coli, cyanotoxins, or a posted beach closure, and a lake with low chlorophyll-a can still bloom. Always check current posted advisories before swimming: water quality changes seasonally, especially in late summer when blue-green algae bloom risk peaks.
How is this ranking calculated?
Lakes are ranked on phosphorus, chlorophyll-a and clarity as measured by EPA and state agency sampling, read against EPA National Lakes Assessment 2022 condition classes for that lake’s ecoregion, not a Minnesota-only 0–100 average. Water clarity is shown beside the nutrient readings. Lakes with limited sampling do not headline the table.
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 25 lakes ranked above have the lowest nutrient and algae readings in our 2026 dataset.
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 →
More on clean water
How nutrient and algae readings are read against EPA ecoregion condition classes, what each class means in the water, and why a clean reading is not a clearance.
The cleanest U.S. lakes under 500 acres, ranked on measured nutrients, algae, and water clarity — with the size cutoff applied to the lake, not the sample.
A practical checklist for picking a lake with good water quality — clarity, phosphorus, algae history, depth, and the data to check before you commit.
Where to stay near Minnesota's cleanest lakes
Compare cabins, resorts, and rentals around Rainy Lake (Cass County, MN) and the other lakes in this ranking, with live availability and prices for your trip. Each pin on the map is one of the ranked lakes above.
Top-rated places to stay near Rainy Lake (Cass County, MN)
Prices for Sep 25–27, 4 adults. Change dates on the map below.
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Source: EPA National Aquatic Resource Surveys, 2026.