Cleanest Lakes in Minnesota & Wisconsin

The top 50 lakes ranked by overall water quality grade. Grades are based on water clarity (Secchi depth in feet), phosphorus levels, and chlorophyll-a (algae) concentration using Metropolitan Council standards.

Across 3,770 monitored lakes in Minnesota and Wisconsin, 45% earn an A grade for water quality and 66% earn an A or B. The top 50 cleanest below split 50 from Minnesota and 0 from Wisconsin — both states draw from the same glacial lake landscape, but Minnesota's deeper Boundary Waters lakes and Wisconsin's spring-fed Northwoods lakes are over-represented at the top.

The cleanest lake on the index is East Fox Lake in Crow Wing County, MN — Grade A, with 16.1 feet of water clarity and phosphorus of 10 µg/L. Below that, the rest of the top 10 fall in a tight clarity band, with the gap between #1 and #10 typically less than three feet of Secchi depth.

All grades come from EPA National Aquatic Resource Surveys and state monitoring programs (MN PCA, WI DNR). Lakes with fewer than three sampling visits are flagged as "limited data." Water-quality grades describe ecology — they do not replace beach-specific E. coli advisories, which your state health department updates separately.

Top 3 Cleanest Lakes

#1A

East Fox Lake

Crow Wing County, MN

The cleanest lake in Minnesota & Wisconsin on our index. Water clarity 16.1 feet, phosphorus 10 µg/L. Max depth 65 ft.

#2A

Deep Portage Lake

Cass County, MN

Second-cleanest with Grade A. Secchi depth 15.4 ft. Max depth 105 ft.

#3A

Little Wabana Lake

Itasca County, MN

Third-cleanest, Grade A. Max depth 57 ft.

Rank	Lake	County	State	Grade	Clarity	Max Depth
1	East Fox Lake	Crow Wing	MN	A	16.1 ft	65 ft
2	Deep Portage Lake	Cass	MN	A	15.4 ft	105 ft
3	Little Wabana Lake	Itasca	MN	A	23.8 ft	57 ft
4	Clearwater Lake	Cook	MN	A	30 ft	65 ft
5	Clearwater Lake	Lake	MN	A	18 ft	46 ft
6	Lower Hay Lake	Crow Wing	MN	A	19 ft	100 ft
7	Latoka Lake	Douglas	MN	A	19 ft	108 ft
8	Bad Medicine Lake	Becker	MN	A	25 ft	84 ft
9	Big Sugar Bush Lake	Becker	MN	A	17 ft	42 ft
10	Pelican Lake	Otter Tail	MN	A	16.1 ft	55 ft
11	Fullers Lake: East Basin	Beltrami	MN	A	49.2 ft	-
12	Birch Lake	Wright	MN	A	15 ft	52 ft
13	Birch Lake	Cook	MN	A	18 ft	69 ft
14	Birch Lake	Unknown	MN	A	15 ft	34 ft
15	Round Lake	Aitkin	MN	A	15.3 ft	59 ft
16	Round Lake	Cook	MN	A	16.5 ft	45 ft
17	Round Lake	Beltrami	MN	A	59.1 ft	-
18	Pike Lake	Cook	MN	A	17.8 ft	45 ft
19	Pike Lake	St. Louis	MN	A	18 ft	60 ft
20	Whitefish Lake	Crow Wing	MN	A	15.1 ft	138 ft
21	Horseshoe Lake	Cass	MN	A	21 ft	51 ft
22	Long Lake	Clearwater	MN	A	20 ft	80 ft
23	Long Lake	Cass	MN	A	21.8 ft	115 ft
24	Long Lake	Beltrami	MN	A	20 ft	87 ft
25	Long Lake	Becker	MN	A	20 ft	61 ft
26	Long Lake	Cass	MN	A	16.8 ft	37 ft
27	Long Lake	Beltrami	MN	A	45.9 ft	-
28	Long Lake	Itasca	MN	A	16.7 ft	72 ft
29	Long Lake	Itasca	MN	A	16.9 ft	85 ft
30	Dead Lake	Hubbard	MN	A	16 ft	34 ft
31	Unnamed Lake	Otter Tail	MN	A	15.1 ft	95 ft
32	Maple Lake	Itasca	MN	A	15.3 ft	39 ft
33	West Twin Lake	Crow Wing	MN	A	19.8 ft	-
34	Sunshine Lake	St. Louis	MN	A	20 ft	37 ft
35	Shallow Lake	Itasca	MN	A	16.4 ft	85 ft
36	Trout Lake	Itasca	MN	A	15.5 ft	135 ft
37	Trout Lake	Itasca	MN	A	18 ft	157 ft
38	Trout Lake	Cook	MN	A	19 ft	77 ft
39	Chippewa Lake	Douglas	MN	A	15.1 ft	95 ft
40	Otter Lake	Otter Tail	MN	A	18 ft	64 ft
41	Eddy Lake	Lake	MN	A	16.5 ft	95 ft
42	Cowdry Lake	Douglas	MN	A	17 ft	52 ft
43	Ossawinnamakee Lake	Crow Wing	MN	A	20 ft	63 ft
44	Clear Lake	Crow Wing	MN	A	18 ft	63 ft
45	Clear Lake	Aitkin	MN	A	16 ft	24 ft
46	Clear Lake	Itasca	MN	A	14.9 ft	30 ft
47	Bear Lake	Lake	MN	A	17.4 ft	31 ft
48	Emerald Lake	Beltrami	MN	A	31.2 ft	-
49	Blue Lake	Hubbard	MN	A	17.4 ft	84 ft
50	Blue Lake	Crow Wing	MN	A	19 ft	48 ft

Frequently Asked Questions

East Fox Lake in Crow Wing County, MN, is the highest-rated lake on our index with a Grade A for overall water quality. Its water clarity (Secchi depth) reads 16.1 feet, with phosphorus at 10 µg/L.

Lakes earn a letter grade A-F based on three metrics from state and EPA monitoring programs: water clarity (Secchi depth in feet — deeper is better), total phosphorus (µg/L — lower is better, since phosphorus drives algae blooms), and chlorophyll-a (µg/L — measures algae directly). Grades use Metropolitan Council water-quality standards.

Of 3,770 lakes in our database, 1,697 (45%) earn an A grade for overall water quality. Another 776 earn a B, bringing the total of A-or-B lakes to 2,473 (66%).

Mostly yes, but not always. Water clarity correlates strongly with low algae and low phosphorus — the same factors that drive harmful algal blooms (HABs). But clarity alone does not measure E. coli, bacterial contamination, or chemical pollutants from runoff. Always check your state agency for current swimming advisories on a specific beach before swimming.

Clean lakes share three traits: low nutrient inputs (especially phosphorus from septic, fertilizer, and farm runoff), good circulation and depth (deeper lakes resist warming and stratification), and protected forested shorelines that filter runoff. The cleanest lakes on this list tend to be deep, far from cropland, and surrounded by undeveloped land.

Worst Water Quality →Clearest Water →Improving →Declining →Best Fishing →