Minnesota is affectionately called the Land of 10,000 Lakes for a reason. Lakes are everywhere!
The state is also home to some of the cleanest lakes in the country and on the entire planet.
Near the Twin Cities and other population centers, the lake’s water quality can be poor. But as you move northward, the water becomes crystal clear. This is especially true in the Boundary Waters Canoe Area Wilderness (BWCA, BWCAW), our favorite place on earth.
Below is a list of 30 of the Cleanest and Clearest Lakes in Minnesota organized by general area. We start in the south around the Twin Cities and work our way north to the Boundary Waters Canoe Area Wilderness.
Is your favorite crystal clear lake missing? Then let us know!
Clearest Lakes in Minnesota – Metro Area
As one would expect, there are not a long of crystal clear waters in the Twin Cities metro area. High population density and high water quality rarely mix. That being said, there area couple of well-known lakes in the are that do make our list of the clearest lakes in Minnesota.
Little Carnelian Lake – Washington County
Little Carnelian Lake is located near Stillwater on the eastern edge of the Twin Cities. It is peculiar in that it has some of the clearest water, but at the same time is on the EPA’s 303(d) list of impaired waters for the high mercury content in fish and is monitored by the Minnesota Pollution Control Agency.
It is one of the few lakes in the area that is popular with both snorkelers and scuba divers!
Clearest Lakes in Minnesota – North East and BWCA
Northern Minnesota is home to a high concentration of the clearest lakes in Minnesota. A large cause is the Boundary Waters Canoe Area Wilderness. That area is off limits to motorized transportation and access is available on a permit-only basis. That protection has led to some of the cleanest and clearest lakes in Minnesota.
We’re biased. It is also our family’s favorite place on earth.
Read More: The Best Boundary Waters Packing List for Canoe Trips
Caribou Lake – Cook County
There are three lakes sharing the same name in Minnesota. This particular lake is located near Lutsen on the North Shore of Lake Superior. It is known for its crystal-clear waters, swimming, water-skiing, fishing, and ice fishing.
Saganaga Lake – Cook County
Saganaga Lake is a large lake that straddles US/Canadian Border. Part of the lake sits inside the Boundary Waters Canoe Area Wilderness boundaries. It is the deepest lake in the area and covers an astonishing 13,832 acres. There are a bunch of great resorts on the eastern side of the lake from which you can enjoy its clean and clear waters.
Read More: 70+ BWCA Entry Points – The Complete List
Namakan Lake – St. Louis County
Namakan Lake is one of the largest and clearest lakes in Minnesota. It straddles the US/Canadian border. We have a friend that owns a cabin on the Canadian side. It is a beautiful north woods lake that is popular with fishermen.
Clearwater Lake – Cook County
Clearwater Lake is another Boundary Waters Canoe Area Lake. It is a long, finger shaped lake that also is home to Clearwater Historic Lodge and Canoe Outfitters. It is an excellent place to experience amazing water quality and the BWCAW.
Read More: 52 BWCA Permit Pick Up Locations – Complete List with Map
Knife Lake – Lake County
Knife Lake is a huge lake that straddles the US/Canadian border. It is often referenced by sections commonly known as Northeastern Knife Lake and South Arm of Knife Lake. The waters are crystal clear and offer excellent fishing.
Fun fact: It was home to Dorothy Molter, who lived on the lake and sold homemade root beer long before the Boundary Waters Canoe Area came into existence.
Read More: 35+ Best Ice Fishing Lakes in Minnesota
Mountain Lake – Cook County
Mountain Lake is a long, narrow lake that straddles the US/Canadian border in the Boundary Waters Canoe Area Wilderness. It is a fun lake to paddle, however can get dangerous on windy days. It is best accessed from Clearwater Lake, which is home to Clearwater Historic Lodge and Canoe Outfitters.
Trout Lake – St. Louis County
Trout Lake is one of the biggest lakes on this list and one of our favorites. My wife’s family lived on Lake Vermilion, and they would take trips to Trout often. It is a big lake with a maze of bays, islands, and peninsulas. The waters are like most in the BWCA, clear and beautiful. Trout Lake is an excellent fishing lake, as is Little Trout Lake, which is also on this list.
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Little Trout Lake- St. Louis County
Little Trout Lake, as one would expect, is located right next to Trout Lake (also on this list) and shares many of the same characteristics. It is accessed via a short portage out of Trout Lake in the northeast corner of the lake.
Missionary Lake – Lake County
Missionary Lake is another crystal clear BWCA Lake. It is located in Lake County, not far from the famous Knife Lake (also on this list). It has clarity of up to 15 feet and that water clarity is maintained all year round. There is a reason it is on this list of the clearest lakes in Minnesota.
Kekekabic Lake – Lake County
Kekekabic Lake is a popular lake in the Boundary Waters Canoe Area Wilderness. It is a large lake just south of Knife Lake and is popular for Lake Trout lake for fishermen. It is also a beautiful lake to visit on a canoe trip.
Ester Lake – Lake County
Ester Lake is a very clear lake with steep shoreline and a rocky bottom. It is best accessed from Saganaga Lake in the BWCA. It has an abundance of coldwater habitat for fish species like lake trout, whitefish, cisco, yellow perch and burbot.
Cherry Lake – Lake County
Cherry Lake is located not far from Ester Lake in the BWCA. It share many of the same characteristics, including being one of the clearest lakes in Minnesota.
Read More: How to Choose the Best Family Canoe in 2024
Bearskin Lake – Cook County
Bearskin Lake is located in northern Minnesota between Lake Superior and the Boundary Waters Canoe Area Wilderness. The lake is so clean that it serves as a control sediment in the federal government’s toxicity tests and was used to develop the US EPA’s toxicity testing methods.
Read More: Minnesota Fishing Trips – Best MN Guides and Charters
Gillis Lake – Cook County
Gillis Lake is a hidden gem tucked away in the Boundary Waters Canoe Area Wilderness. It is the third-deepest lake in the BWCAW at 180 feet. If you are looking to fish, beware. Outside of burbot and bait fish, it is primarily a lake trout lake.
Clearest Lakes in Minnesota – Central Region
The middle of the state for many is true cabin country. It is dotted with beautiful lakes of all shapes and sizs. What many do not realize is that many of these lakes compete with the Boundary Waters for the cleanest and clearest lakes in MN.
East Twin Lake – Crow County
East Twin Lake is a smaller lake in Crow County outside of the town of Nisswa. The lake is quite deep, which contributes to the clarity of the water. Unlike many in this section, it is not in the BWCA, so it is easier to access without a permit.
Big Bass Lake – Hubbard County
Big Bass Lake is located south-west of Leech Lake near the town of Akeley. It is an excellent fishing lake and has excellent water clarity with a secchi depth of 15-18 feet and a large portion of undeveloped shoreline.
Big Sand Lake – Hubbard County
Big Sand Lake is located next to one of our favorite state parks, Savannah Portage State Park. It is well known as an excellent fishing lake that is less busy than popular lakes like Leech Lake. It is less well known that it is also one of the clearest lakes in Minnesota. We love Big Sandy Lake’s pristine waters.
Read More: Guide to Planning Epic Ice Fishing Trips in Minnesota
Hunter Lake – Cass County
Hunter Lake is another surprisingly clean and clear lake. Don’t let it’s shallow depths fool you. The water clarity is incredible. It is located just south of Leech Lake and in the Walker area.
Deer Lake – Itasca County
Deer Lake is an incredibly clear lake, however the long-term trend for water quality is on the decline. These clean and clear waters support abundant wildlife. Hopefully some careful management can stop the decline and bring back its former glory.
Deer Lake is located just north of Grand Rapids, MN.
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Ossawinnamakee Lake – Crow Wing County
Lake Ossawinnamakee has crystal clear waters all summer long. It is located in the Pequot Lakes area, north of Gull Lake and south of Lower Whitefish Lake. It is a long, narrow lake that almost gets lost among the larger lakes in the area.
Eleventh Crow Wing Lake – Hubbard County
Eleventh Crow Wing Lake is a deep lake with excellent water quality. It is located near Big Bass Lake, another lake on our 30 Cleanest and Clearest Lakes in Minnesota list. We’ve heard the fishing is excellent.
Three Island Lake – Itasca County
Three Island Lake is part of the Turtle River chain of lakes, northeast of Leech Lake. It is well known for large walleye, largemouth bass, northern pike, and panfish populations. The water is clean and clear and it is a popular lake on windy days when the larger lakes in the area are too choppy.
Bad Medicine Lake – Becker County
Bad Medicine Lake is fed by underground springs and is located near Itasca State park. It is no wonder it is Minnesota’s best known rainbow trout fishery. It got its name from the Native Americans, who thought that because it had no inlet or outlet that it brought bad omens. As a result, they would not hunt or fish at or near the lake.
Boot Lake – Jackson County
Boot Lake is well known for its clear water and undeveloped shoreline. A Secchi Disk reading of 19-27 puts it high on the list of the clearest lakes in Minnesota. It is located near the White Earth Reservation in the north central part of the state.
East Crooked Lake – Hubbard County
East Crooked Lake is located near the town of Nevis near Park Rapids. It has exceptionally clear waters and is best known for walleye fishing. It also has large populations of northern pike, smallmouth bass, largemouth bass, and panfish.
Clearest Lakes in Minnesota – Abandoned Mines
It might be surprising, but abandoned mines often have clearer water than many of Minnesota’s lakes. They also generlaly have miles of shoreline with cliff jumbing spots.
Read More: 60+ Best Hiking Trails on Minnesota’s North Shore
Fraser Pit – St. Louis County
Fraser Pit is an abandoned open pit mine located near Chisholm, MN. The water clarity is so great that the City of Chisholm currently draws its municipal water from the lake.
Sabin (Embarrass Mine) Lake – St. Louis County
Anothe abandoned open pit mine, Sabin Lake (Embarrass Mine) is home to crystal clear waters and a unique surrounding. It is a popular local spot for swimming. It is located near Embarass, Minnesota.
Jessie Pit – Itasca County
Jessie Pit, another abandoned open-pit mine, is rumored to have the second-best water quality in the state. It is a popular spot for swimmers and cliff jumpers due to its clear water and depth. It is located just outside of Grand Rapids, MN.
