Top 15 Places to Fly Fish in Minnesota – And What Flies to Use

Top 15 Places to Fly Fish in Minnesota – And What Flies to Use

Minnesota is a great destination for fly fishing. Of all of the waterways in the state, it is hard to choose just 15, but these are some of the best places to fly fish in Minnesota. Keep reading to discover the 15 best of the best spots to fly fish in the Land of 10,000 Lakes.

Minnesota is a great destination for fly fishing, with more miles of shoreline than Hawaii, California, and Florida combined. The state's over 6,500 lakes, rivers, and streams provide anglers with more than 69,0000 miles of water, an abundance of fish, and some of the most stunning views in the United States.

Some of the best places to fly fish in the state of Minnesota include: 

  • Cross River
  • French River
  • Root River
  • Croix River
  • Stoney Brook
  • Temperance River, and
  • Trout Run Creek and more
Lake Trout with Minnesota State Flag

Of all of the waterways in the state, it is hard to choose just 15, but these are some of the best places to fly fish in Minnesota. Keep reading to discover the 15 best of the best spots to fly fish in the Land of 10,000 Lakes. 

Best Fly Fishing locations in Minnesota

Badger Creek Minnesota Fly Fishing

1. Badger Creek, Houston County, MN

Badger Creek, a tributary of the South Fork Root River in Houston County, Minnesota, has been given its name due to the abundance of badgers that used to roam this area. This majestic stream is located east of Houston and offers breathtaking views for visitors and locals alike.

According to the Minnesota Department of Natural Resources, Badger Creek is teeming with life, home to a variety of fish species, including:

  • Brown trout
  • Brook trout
  • White sucker and
  • Creek chub.

Additional inhabitants include southern redbelly dace, northern redbelly dace, and blacknose dace alongside longnose dace, bluntnose minnow, fathead minnow, common shiner, and bigmouth shiner. In 1970, improvements to the upper-Badger Creek habitat were completed to keep it as a wild trout fishery. Brown trout stocking was discontinued two years later, and brook trout stocking ended likewise by 1974.

Fly Patterns for the Badger Creek, Minnesota

Recommended Fly Patterns for the Badger Creek, Minnesota:


Baptism River Minnesota Fly Fishing

2. Baptism River

Stretching 8.8 miles through the beautiful U.S. state of Minnesota, the Baptism River is a stunning landmark that originates from the joining of two rivers - East Branch and West Branch Baptism - near Finland's community.

The spectacular High Falls of the Baptism River in Tettegouche State Park is Minnesota's highest waterfall. Towering at a thrilling 60 feet (18 m) tall, they exceed even that of Ontario's Pigeon River! Furthermore, this stunning river serves as a designated trout stream and is home to various types of trout and Chinook salmon.

Fly Patterns for the Baptism River, Minnesota

Recommended Fly Patterns for the Baptism River, Minnesota:


Boundary Waters Minnesota Fly Fishing

3. Boundary Waters

If you're searching for some of Minnesota's best fishing spots, look no further than the Boundary Waters Canoe Area Wilderness! U.S. Forest Service manages this 1.09 million acre preserve located within Superior National Forest, and it's teeming with game fish, including:

  • Northern pike
  • Walleye
  • Largemouth bass, and
  • Smallmouth bass

The Boundary Waters is an untarnished wonder with no roads or structures. Motors are restricted to only some bodies of water for a truly tranquil experience. It stands as the biggest Wilderness east of the Rockies and north of the Everglades, making it one of America's most accessible outdoor recreational areas!

If you're looking for some of the best trout fishing opportunities, then this wilderness is your destination. Here, anglers can find all types of trout, such as brook trout, lake trout, rainbows, and splake.

Walleye and Lake Trout stocking has also been limited in certain areas due to natural recruitment issues allowing it to become one of the largest concentrations of native lake Trout lakes found throughout the lower 48 states.

Fly Patterns for the Boundary Waters, Minnesota

Recommended Fly Patterns for the Boundary Waters, Minnesota:


Cannon River Minnesota Fly Fishing

4. Cannon River

The majestic Cannon River is a tributary of the mighty Mississippi River. It runs for 112 breathtaking miles (180 km), starting from Shields Lake by Shieldsville to Red Wing in Minnesota, where it converges with the river.

Spanning a massive 1,460 square miles (3,780 km²) over Le Sueur County, Rice county, Dakota, and Goodhue counties is the Cannon River. It doesn't contain too many difficult rapids to maneuver around (Class II). Still, they have caused fatalities in certain circumstances - such as at its confluence with the Little Cannon River near Cannon Falls.

From Faribault and upstream, the most frequently caught fish in reservoirs and slower parts of the river are northern pikes, black crappies, bluegills, and bullheads. Going downstream from there, one is likely to come across smallmouth bass, walleyes, or channel catfish--the latter especially so in the area below Cannon Falls.

Fly Patterns for the Cannon River, Minnesota

Recommended Fly Patterns for the Cannon River, Minnesota:


Cenaiko Lake at Coon Rapids Dam Regional Park Minnesota Fly Fishing

5. Cenaiko Lake at Coon Rapids Dam Regional Park

Nestled within Coon Rapids Dam Regional Park and run by Anoka County Parks, Cenaiko Lake is an awe-inspiring 28.5-acre manmade lake with a depth that plunges 36' at its deepest points! Ample parking, walking trails around the lake, and two fishing piers maintained by Anoka County make this spot ideal for exploring nature's beauty. 

If you're an avid angler, Cenaiko Lake is the perfect fishing spot! With its special designation as a stream trout lake, only those with a current trout stamp are allowed to fish here during designated season times.

Plus, any other type of fishing besides catching trout is prohibited when the regular season has ended. There is no boat access on this lake. However, a fishing pier is available for use. You'll find an abundance of fish species in Cenaiko Lake, including:

Annually, the lake is stocked with 2,000 Rainbow Trout yearlings each spring and an additional 3,000 in fall. Surplus adult Brook or Rainbow Trout are stocked when available to further enhance the trout population within the lake.

Fly Patterns for the Cenaiko Lake at Coon Rapids Dam Regional Park,

Recommended Fly Patterns for the Cenaiko Lake at Coon Rapids Dam Regional Park, Minnesota:


Cloquet River Minnesota Fly Fishing

6. Cloquet River

The Cloquet River in northeastern Minnesota is an ideal destination for fishing and paddling enthusiasts. Visitors will encounter class 1-3 rapids while they navigate along its heavily forested banks throughout most of its upper stretch; however, as travelers move downriver, the landscape transitions to partially wooded areas alongside farmland and residences.

Though thrilling fun awaits at every turn on this trail, it's important to be aware that certain steep rocky sections may become impassable if water levels are low. The Cloquet River gives anglers the opportunity to catch:

  • Brook trout
  • Brown trout
  • Walleye
  • Channel catfish
  • Smallmouth bass
  • Sunfish, and
  • Northern pike

Fly Patterns for the Cloquet River

Recommended Fly Patterns for the Cloquet River, Minnesota:


Cross River Minnesota Fly Fishing

7. Cross River

The Cross River, spanning a length of 20.4 miles (32.8 km) in the United States' northern Minnesota region, is an immediate branch of Lake Superior. Just southwest of Temperance River State Park lies Cross River Falls, where you can witness the river's rapid descent beneath Highway 61's bridge!

To truly appreciate the beauty of the upper part of the falls, simply park on the southwest side and take a leisurely stroll across the bridge. The sight alone is sure to leave you in awe! When it comes to fly fishing the Cross River, anglers are likely to come across:

  • Brook trout
  • Pink salmon
  • Rainbow Trout
  • Walleye
  • Smallmouth bass, and
  • Northern pike.

Fly Patterns for the Cross River, Minnesota

Recommended Fly Patterns for the Cross River, Minnesota:


French River Minnesota  Fly Fishing

8. French River

French River is a beautiful unincorporated yet vibrant community in Duluth Township, Saint Louis County of Minnesota. You can find yourself at the junction of North Shore Scenic Drive (County 61) and Ryan Road (County Road 50), 13 miles northeast of Duluth. Lakes Superior's magnificent North Shore streams offer a remarkable fishing experience with special regulations depending on which boundary they are posted to.

Drifthook Fly Fishing Flies Kits for Minnesota

The French River, situated in St. Louis County and northeast of Duluth, entices anglers with its 12.9-mile stretch leading to Lake Superior. Starting from the upper reaches of Pioneer Road is a mixture of grassy wetlands and wetland forests boasting silt substrates that transition downstream into upland forests with cobble, gravel, and boulder beds for added difficulty when locating fish habitats.

From Muskie to Walleye, Largemouth Bass to Smallmouth Bass, and Northern Pike, the French River is a haven for all kinds of species.

Fly Patterns for the French River

Recommended Fly Patterns for the French River, Minnesota:


Root River Minnesota Fly Fishing

9. Root River

Meandering through the picturesque Driftless Area of southeastern Minnesota, the Root River flows for an impressive 80 miles (130 km) before culminating in a junction with the Upper Mississippi. Formed by three branches - North, South, and Middle- and the South Fork Root River, this idyllic river is ideal for canoeing and fishing enthusiasts alike.

With its pleasant to moderate current gradually descending 3.4 ft/mile from Chatfield to La Crosse's Navigation Pool 7 on Wisconsin's border near Hokah, Minnesota, the Root River offers fly fishing opportunities for a variety of species including:

  • Brown Trout
  • Rainbow Trout
  • Smallmouth Bass
  • Rock bass
  • Channel catfish, and
  • Crappie

The Root River system is alive with the presence of shorthead redhorse, river redhorse, golden redhorse, silver redhorse, Longnose Sturgeon, and greater redhorses, to name a few.

The area's avian population includes such wildlife species as majestic bald eagles soaring overhead; blue herons gracefully gliding through the sky; wild turkeys strutting along the ground levels; and wood ducks floating on their peaceful waters below.

Fly Patterns for the Root River, Minnesota

Recommended Fly Patterns for the Root River, Minnesota:


St. Croix River Minnesota Fly Fishing

10. St. Croix River

Named for the French phrase "holy cross," The St. Croix River spans a breadth of 169 miles and flows through both Wisconsin and Minnesota, with its last 125 miles forming the border between these two states. Recognized as an intrinsic natural wonder, this river is proudly protected by the National Park Service under its national scenic riverway title.

Generating renewable energy, the Saint Croix Falls Dam hydroelectric plant electrifies Minneapolis–St. Paul and its surrounding area with power from nearby water flow. Fishermen flock to these waters for walleye, sauger, smallmouth bass, and many other species like sturgeon, muskellunge, white bass, and catfish, offering plenty of chances for a successful catch.

Fly Patterns for the St. Croix River, Minnesota

Recommended Fly Patterns for the St. Croix River, Minnesota:


Stony Brook Minnesota Fly Fishing

11. Stoney Brook

Stoney Brook Township is a vibrant township located in Grant County, Minnesota, and was established in 1877. Nestled in the center of Minnesota, Stoney Brook is a shady brook trout stream that leads to Upper Gull Lake near Brainerd. Although its average size width is about 22 feet, the rocky riffles and runs make up for its lack of size.

Even though this isn't what one would consider an "ideal" fishing destination like some other streams such as The South Branch of Root or Straight River on M.N. North Shore, the DNR has done their part by improving fish habitat with special regulations prohibiting harvesting brook trout from these waters.

If you want to catch some trout, Fritz Loven Park and a tiny pull-off along County Rd 78 offer access. MN DNR fishing easements are scattered throughout the primary reach of this aquatic area, with the exception of Section 8's southwest corner. Not only is there potential for abundant trout at Fritz Loven Park, but it also provides picnic areas and trails!

Fly Patterns for the Stony Brook, Minnesota

Recommended Fly Patterns for the Stony Brook, Minnesota:


Temperance River Minnesota Fly Fishing

12. Temperance River

The Temperance River is an impressive 39.2-mile stretch of water that winds its way through northern Minnesota, beginning at the serene Brule Lake and ending with a splash into Lake Superior right near Tofte. Along the course of this river lies temperate rainforests, cascading rapids, and stunning rock formations - all within the boundary lines of Temperance State Park!

Brule Lake is a rarity that has two streams leaving it - the Temperance from its western outflow and the South Brule River from its eastern outlet. The former carries about half of all water released by the lake, while for practically all of its initial course, the latter flows through a set of smaller lakes.

If you venture upstream of the Temperance River, you'll find a thriving cool water fishery that is teeming with walleyes, smallmouth bass, yellow perch, and a few other species native to this region. These fish are not confined within just the lakes adjacent to the river as they can be spotted swimming through its waters too!

Recommended Fly Patterns for the Temperance River, Minnesota:

Recommended Fly Patterns for the Temperance River, Minnesota:


Trout Run Creek Minnesota Fly Fishing

13. Trout Run Creek

Situated in western Winona County, Trout Run Creek sprawls through the Whitewater watershed and flows into the Middle Branch of the Whitewater River. Its nearest town is St. Charles, making it a favorite spot for avid park visitors and campers alike.

Furthermore, its Brown trout fingerling abundance has been found to be quite remarkable - indicating that Trout Run likely acts as an essential spawning/nursery area for fish living within the Middle Branch of the Whitewater River.

Beautiful, spring-fed Trout Run Creek stretches across 12 miles of the prairie Minnesota landscape before joining forces with the North Branch of Root River. An assessment conducted last year showed that brown trout biomass ranged from 51 to 314 pounds per acre - up to 100 fish measuring over 12 inches each mile! Whether you're a fisherman or just looking for somewhere peaceful and picturesque, this is one spot you won't want to miss out on.

Trout Run is renowned for its endless opportunities to catch monster brown trout. With plenty of cover, deep pools, and undercut banks, it's no wonder the stream has a population estimated to range between 2,000-4,000 per mile! The tranquil river drifts through hardwood trees and open meadows - making this spot an angler's paradise.

Fly Patterns for the Trout Run Creek, Minnesota

Recommended Fly Patterns for the Trout Run Creek, Minnesota:


Vermillion River Minnesota Fly Fishing

14. Vermillion River

Meandering through Scott and Dakota Counties in Minnesota, the 59.6-mile (95.9 km) Vermillion River eventually arrives at a Mississippi River floodplain that is situated just south of Hastings. Of this river's length, 13.5 miles (21.7 km) are designated as trout stream habitat - an extraordinary feat being so close to a metropolitan area.

This means anglers have the chance to catch trophy-sized specimens while enjoying all there is on offer from this unique environment near Minneapolis/St Paul Metro Area.

The Vermillion River makes a perfect spot for catch-and-release fishing of brown trout and is managed specifically as such by the state. The ideal location to try your luck lies upstream around Farmington, Empire, and Lakeville. However, after the waterfall in Hastings, warm temperatures make it an unsuitable habitat for trout - so keep heading south if you're looking to target northern pike or freshwater drum.

Fly Patterns for the Vermillion River, Minnesota

Recommended Fly Patterns for the Vermillion River, Minnesota:


Whitewater River Minnesota Fly Fishing

15. Whitewater River

Located in the Driftless Area of Minnesota, the Whitewater River is a breathtaking 16.6-mile (26.7 km) tributary that eventually meets with the Upper Mississippi River by Weaver, Wabasha County - near Altura, Saint Charles, and Elba townships. This magnificent destination holds many natural wonders; its unique dry oak savannas are on the brink of extinction due to their reliance on fire for rejuvenation.

Where the North Fork Whitewater River and Middle Fork Whitewater River meet at Elba lies the main stem of the majestic Whitewater. Just downstream, this wonderful river is joined by its South Fork counterpart.

The Upper branches of this waterway, which wind through beautiful Whitewater State Park, are home to abundant trout populations - including native brookies and wild browns, as well as rainbow trout that have been stocked in certain areas. These streams boast an impressive channel length of 47 km (or c. 30 miles).

Fly Patterns for the Whitewater River, Minnesota

Recommended Fly Patterns for the Whitewater River, Minnesota:


Rainbow Trout

What Gear do I need to Fly Fish in Minnesota?

Minnesota fly anglers should bring along a 5 or 6-weight rod with a matching reel and floating line for general trout fishing - although this will depend on your specific target species. Leaders, tippets, waders, and flies are essential, along with other items, such as polarized sunglasses, to reduce glare from the water's surface.

Fly Fishing Gear for Minnesota

Additionally, you will need waders to stay dry while fishing in shallow streams. A landing net is also essential for safely releasing your catch back into the water. It's important to be equipped with an appropriate tackle box containing all necessary items, such as lures and flies,

Additional Facts about Fly Fishing in Minnesota

Fly fishing in Minnesota is legal all year round, with few exceptions. However, the best times to target the different species of fish depend on the time of year - for example, brown trout tend to bite more during colder months, while some bass species are more active in warmer weather.

It is also important to note that many areas have catch-and-release regulations - so be sure to check the local rules before casting your line. It is also important to remember that certain bodies of water are closed during specific times or even entirely due to conservation efforts to protect the native fish species.

Where is the best trout fishing in M.N.?

The Driftless Region is an expansive 4,000-square mile expanse across Southeast Minnesota, Southwest Wisconsin, and Northeast Iowa - undeniably the most ideal region in Minnesota for trout fishing.

Amazing trout fishing in Minnesota is also found in the many tributaries of the Mississippi River, including smaller streams and larger rivers such as the Vermillion. Other great spots include Lake Superior’s North Shore, where anglers can find cold water species like brook and rainbow trout.

Best Dry Flies to Catch Trout

Does Minnesota have good fly fishing?

Minnesota is a great fly fishing destination. The state is home to many rivers and streams that are perfect for anglers of all levels, from beginners to experts. While the state's renowned Driftless Region offers some of the best trout fishing in the country, Minnesota also boasts abundant bass, pike, walleye, and panfish populations.

Minnesota is a great destination for fly anglers of all skill levels. This state has something for everyone, from the Upper Mississippi River to Lake Superior's North Shore. Be sure to check local fishing regulations and practice catch-and-release if needed.

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