Fly Fishing in Minnesota: 14 Top Destinations You Need to Fish

Key Takeaways:

  • Minnesota offers diverse fly fishing opportunities, including renowned spots like Badger Creek, Baptism River, and Boundary Waters, each teeming with various trout species and scenic landscapes.
  • The prime season for fly fishing in Minnesota is during spring, with late April to early June being ideal for trout in rivers like Baptism and Cloquet, and summer is perfect for Boundary Waters for bass, pike, and trout.
  • Minnesota’s waters boast trout, smallmouth bass, and northern pike, making it an excellent destination for fly anglers looking for diverse challenges.
  • Fishing regulations include the requirement of a fishing license for most anglers aged 16 to 89, catch-and-release rules for trout in early spring, and specific rules for certain species like muskies.
  • To stay up-to-date on fishing rules, it’s essential to regularly check with the Minnesota Department of Natural Resources, as regulations may vary based on local conservation efforts.

List of the 14 Best Places to Fly Fish in Minnesota

List of the 14 Best Places to Fly Fish in Minnesota

From lakes and streams to rivers, Minnesota offers a variety of fly fishing opportunities. Anglers of all levels can enjoy the thrill of fly fishing in Minnesota. Here are some of the best places:

  • Badger Creek, Houston County
  • Baptism River
  • Boundary Waters
  • Cannon River
  • Cenaiko Lake within Coon Rapids Dam Regional Park
  • Cloquet River
  • Cross River
  • French River
  • Root River
  • St. Croix River
  • Temperance River
  • Trout Run Creek, St. Charles
  • Vermillion River, Farmington
  • Whitewater River, Weaver

1. Badger Creek, Houston County

  • The Badger Creek flows through Houston County in the U.S. state of Minnesota. It’s a South Fork Root River tributary located east of Houston, Minnesota.
  • This serene stream is abundant with native fish species, and its upper habitat has been preserved as a wild trout fishery, making it a popular destination for catching brown trout and brook trout.
  • Badger Creek’s stunning views and crystal-clear waters are a feast for the eyes. It’s also home to various types of dace, shiner, and bigmouth shiner, making it a diverse and thriving ecosystem.

2. Baptism River

  • Baptism River runs 8.8 miles through Minnesota. In Finland, two branches of the Baptism River meet just south of the river’s source.
  • The beautiful river is a designated trout stream rich in various trout and Chinook salmon types. Its standout feature is the spectacular High Falls, which is tall at 60 feet and exceeds even Ontario’s famous Pigeon River.
  • Stunning scenery of this river and its surrounding areas is unparalleled. With breathtaking waterfalls, serene rapids, and deep pools, the Baptism River has something for everyone.

3. Boundary Waters

  • In northeastern Minnesota, the Boundary Waters Canoe Area Wilderness lies in the Superior National Forest, managed by the US Forest Service.
  • There are a lot of game fish species in the Boundary Waters Canoe Area Wilderness, including walleye, northern pike, smallmouth bass, largemouth bass, and trout.
  • The fact that there are no roads or structures and that motors are restricted to some bodies of water adds to its serene vibe. Fishing in this untarnished wilderness is a once-in-a-lifetime experience that every angler should have on their bucket list.

4. Cannon River

  • From Shields Lake near Shieldsville to Red Wing in Minnesota, where it meets the Mississippi River, the Cannon River flows 112 miles. About 1460 square miles of watershed are drained by it.
  • You can look forward to catching a range of species, and the river is beautiful any time of the year. Northern pike, black crappie, bluegill, bullhead, smallmouth bass, walleyes, and channel catfish are among the most commonly caught fish in this area.
  • The Cannon River’s stunning 112-mile stretch is nestled in Le Sueur County, Rice County, Dakota, and Goodhue counties, home to ample aquatic life.

5. Cenaiko Lake within Coon Rapids Dam Regional Park

  • Anoka County Parks operates Coon Rapids Dam Regional Park with Cenaiko Lake. There’s a 28.5-acre man-made lake here with a maximum depth of 36 feet.
  • Crystal-clear waters make Cenaiko Lake a sight to behold. Among the fish you can catch here are Rainbow Trout, Hybrid Sunfish, and Smallmouth Bass.
  • This lake has walking trails, fishing piers, and ample parking. Head here with your trout stamp and enjoy an exclusive fishing experience.

6. Cloquet River

  • Minnesota’s Cloquet River runs 104 miles. It is one of the main tributaries of the Saint Louis River.
  • You’ll find Brook Trout, Brown Trout, Walleye, Channel Catfish, Smallmouth Bass, and Northern Pike in partially wooded areas bordering farmland and houses.
  • The winding Cloquet River, complete with class 1-3 rapids in its upper stretch, offers fantastic fishing and paddling opportunities. While it’s an adventure at any time of year, be aware that certain sections may be impassable if water levels are low.

7. Cross River

  • In northern Minnesota, Cross River flows for 20.4 miles before becoming an immediate branch of Lake Superior.
  • There are numerous species of fish to be found in Cross River, including brook trout, pink salmon, rainbow trout, walleye, smallmouth bass, and northern pike.
  • Cross River Falls is a must-visit spot where you can witness the river’s rapid descent beneath Highway 61’s bridge. Don’t forget to try out the recommended fly patterns of Zebra Midge Black and Zonker to increase your chances of catching some amazing fish.

8. French River

  • French River is an unincorporated community in Duluth Township, Saint Louis County, Minnesota. It can be found at the junction of North Shore Scenic Drive (County 61) and Ryan Road (County Road 50), 13 miles northeast of Duluth.
  • The French River is a 12.9-mile stretch leading to Lake Superior and offers a remarkable fishing experience for various species such as muskie, walleye, largemouth bass, smallmouth bass, and northern pike.
  • You can find premium hand-selected fishing flies to catch more fish conveniently available for purchase. The upper reaches of Pioneer Road provide a mixture of grassy wetlands and wetland forests with silt substrates.

9. Root River

  • Root River flows 80 miles across the picturesque Driftless Area of southeastern Minnesota before culminating at the Upper Mississippi.
  • The Root River is a fly fisher’s haven with a pleasant to moderate current that gradually descends 3.4 ft/mile. This offers fly fishing opportunities for brown trout, rainbow trout, smallmouth bass, rock bass, channel catfish, and crappie.
  • This river system is alive with various redhorse species and Longnose Sturgeon. The area’s avian population includes bald eagles, blue herons, wild turkeys, and wood ducks.

10. St. Croix River

  • Spanning 169 miles, the St. Croix River is a natural wonder that borders both Wisconsin and Minnesota.
  • Fishermen flock to this river for its abundance of fish species, including walleye, sauger, smallmouth bass, and more- a perfect location for a successful catch.
  • It’s home to the Saint Croix Falls Dam hydroelectric plant, generating renewable energy to power Minneapolis-St. Paul and its surroundings.

11. Temperance River

  • The Temperance River stretches an impressive 39.2 miles through northern Minnesota, starting at Brule Lake and ending with a plunge into Lake Superior.
  • You can catch Walleye, Smallmouth Bass, Yellow Perch, and other species. Try using Parachute Mahogany Duns, Parachute Adams recommended fly patterns for the best catches.
  • Along the course lies temperate rainforests, cascading rapids, and stunning rock formations, all within the boundaries of Temperance State Park.

12. Trout Run Creek, St. Charles

  • Located in western Winona County, Trout Run Creek sprawls through the Whitewater watershed and flows into the Middle Branch of the Whitewater River.
  • The tranquil river drifts through hardwood trees and open meadows, making it a picturesque spot to catch a monster brown trout.
  • Beautiful, spring-fed Trout Run Creek stretches 12 miles of the prairie Minnesota landscape up to 100 fish measuring over 12 inches each mile. With plenty of cover, deep pools, and undercut banks, this spot is an angler’s paradise. 

13. Vermillion River, Farmington

  • Meandering through Scott and Dakota Counties in Minnesota, the 59.6-mile Vermillion River eventually arrives at a Mississippi floodplain just south of Hastings.
  • It’s the perfect spot for catch-and-release brown trout fishing, with anglers being able to catch huge trout while enjoying this picturesque environment close to Minneapolis/St Paul.
  • The optimum location to catch fish lies upstream around Lakeville, Farmington, and Empire. Keep moving south if you want to target northern pike or freshwater drum.

14. Whitewater River, Weaver

  • The Whitewater River is a 16.6-mile tributary in the Driftless Area of Minnesota in Weaver, Wabasha County, near Altura, Saint Charles, and Elba townships.
  • The Upper branches of this waterway, passing through Whitewater State Park, contain a large trout population. This includes native brookies, wild browns, and rainbow trout stocked in certain areas. 
  • The unique dry oak savannas surrounding the river are truly a sight to behold and add to the beauty of the fishing experience.

What is the ideal time of year to fly fish in Minnesota?

During spring, late April to early June is the prime time to hit the rivers and streams. The cool temperatures of early mornings and late afternoons are perfect for fishing steelhead and trout. The Baptism and Cloquet Rivers are popular spots but don’t overlook Cenaiko Lake for trout.

Summer presents its challenges since the midday heat reduces fish activity. Your best bet is to hit the Boundary Waters area for bass, pike, and trout during the early mornings and evenings when temperatures are cooler. St. Croix River is also great for smallmouth bass and other warm water species.

As autumn approaches, the mornings get cooler, and the fish become more active. Late mornings and early afternoons are the sweet spot for rivers and streams such as Root River and Trout Run Creek for trout. The Vermillion River is an excellent choice for brown trout.

Winter fly fishing in Minnesota can be tough, but you can still catch species like trout by ice fishing on lakes and rivers. Late mornings are your best bet after the sun has warmed the water slightly, and always take extra safety precautions.

What kind of fish can I catch with fly fishing in Minnesota?

What kind of fish can I catch with fly fishing in Minnesota

Minnesota is known for its trout fishing, and you can find both brown and brook trout in its streams and rivers. Locations like Badger Creek, Root River, and Whitewater River are popular spots for trout enthusiasts.

Smallmouth bass and northern pike are abundant in Minnesota waters, including the St. Croix River and Boundary Waters. These species provide exciting fly fishing challenges.

The Baptism River allows Chinook salmon to catch using fly fishing methods, especially in its scenic surroundings. Minnesota also allows fly fishing enthusiasts to target species like catfish, crappie, and sunfish in various bodies of water, making it a well-rounded destination for diverse fly fishing experiences.

What are the fly fishing rules & regulations in Minnesota?

  • A fishing license is required for anyone aged 16 to 89 unless an exemption applies.
  • Fishing licenses are effective from March 1 to the last day of February of the following year.
  • When angling for trout, catch and release is only allowed from January 1 until Saturday.
  • No more than nine inches must be between the first and last hook.
  • Live, artificial, preserved, or dead bait is allowed.
  • Only one line is allowed in winter or summer when fishing on designated stream trout lakes and designated trout streams.
  • For most inland trout anglers, Spring and early Fall are recommended as peak seasons.
  • Speakers, anglers, and bowfishers can keep up to 10 gars, the toothy, prehistoric fish native to Minnesota waters.
  • No more than 1 may be over 16 inches in length for certain fish species.
  • For muskies, the limit is 1 per calendar year, and the fish must be between 45-50″ inclusive or over 75″. Catch-and-release only from Oct 1 – April 23 of the following year. No tag is needed.

#Please Note: These rules can change based on local conservation efforts and should be checked regularly with the Minnesota Department of Natural Resources.