Michigan Fly Fishing 5 min read

DIY Guide to Fly Fishing the Thunder Bay River in Michigan

Ken Sperry

Posted by Ken Sperry

March 1, 2022

Thunder Bay River lighthouse in Michigan.

For those who have never spent time in Alpena, Michigan, you might only know that it is home to the Thunder Bay River. However, this city is known as the Sanctuary of the Great Lakes and offers all sorts of fishing, boating, and watersports fun. It’s the perfect spot to start a fishing expedition for anyone who wants to experience the beauty of northeast Michigan.

When you spend time at Thunder Bay River, you can enjoy catching various fish, including brown trout, salmon, steelhead, smallmouth bass, and more. Not only are there pristine clear waters, but all sorts of beaches, parks, and other attractions.

About Thunder Bay River

A view of the Thunder Bay River near Hillman, Michigan.  Some of most productive trout fishing is located upstream from Hillman to Atlanta, Michigan.

Thunder Bay River spans a distance of more than 75 miles across Michigan. The majority drains in Montmorency and Alpena Counties and a bit in Oscoda County, into Thunder Bay on the eastern area of North Michigan. You can trek to the stream’s mouth from downtown Alpena where it is protected by the Alpena Light Station.

Unique from most rivers in the state, this stream drops a huge amount from the headwaters to Lake Huron. The upper and middle reaches are largely concentrated in Mackinaw State Forest, making it a popular destination for anyone who wants to catch trout. The forest is filled with birch and aspen trees and offers encounters with local wildlife.

Being inside of a state forest, anglers will find several sites for camping or parking small trailers. All of the sites have access to the water, making them a great option for fly fishers who want to save money on lodging. The campground is rustic and includes a hand pump, vault toilets, and pathway access.

The Thunder Bay River has dozens of dams that slow the river and create varied habitat. Many of them are small and located on tributaries, but some are storage reservoirs and hydropower dams. There are many types of fish throughout the river, but the most common are trout, smallmouth bass, salmon, and steelhead. This makes the river an excellent location for fishing in any season.

Keep in mind that Thunder Bay River has several branches including the North Branch, Mainstem and Upper and Lower South Branches.

The North Branch is too warm for trout as is the lower Mainstem below the Hillman Dam.  The Upper South Branch is fed by groundwater and harbors a good population of trout but is most lined by private property.  The Lower South Branch is an excellent smallmouth bass fishery.

Steelhead, Chinook, coho and pink salmon make annual runs up the short stretch of water from Lake Huron to the Ninth Street Dam.

Thunder Bay River Map and Fishing Access Sites

Map of the best fishing spots on the Thunder Bay River in Michigan.

Get Directions to the Fishing Access Points shown above with the DIY Fly Fishing Map

Best Places to Fish the Thunder Bay River

A top location for steelhead and salmon fishing is at the 9th Avenue Dam in Alpena.

It’s only a mile away from Lake Huron’s Thunder Bay and is the only area that is fully accessible to freshwater fish migrating away from Lake Huron. This is a designated trout stream where you can fish by wading or on the rocky shore.

The best, and least-pressured, trout waters are located on the Mainstem from Atlanta to Hillman.  The MDNR stocks brown trout annually from Atlanta to M33.  You’ll also find some brookies here as well.

Lake Winyah is on Thunder Bay River and offers access to the river channel near the dam and many fish, including walleye. Pike are often available in the early season’s shallow waters, but bigger fish are found later in the season in the deeper waters. Smallmouth bass, crappies, bluegills, and other fish are also located in this area.

The final destination to consider is the Thunder Bay National Marine Sanctuary, which protects hundreds of shipwrecks off the city’s coast. Many fish species use the debris as homes and tend to be different species than you could expect to find in the inland lakes.

Best Time to Fish the Thunder Bay River

The Thunder Bay River has many runs of large lake fish in both the fall and spring. 

The Salmon start running upriver in late August and continue as late as October.  Atlantic Salmon are a recent success story due to aggressive stocking by the state and see excellent fall runs.

The fall steelhead run typically peaks in November with occasional lake-run brown trout.  Another excellent run of steelhead occurs in the spring.

Trout fishing is best in the spring and fall.  Water temperatures get a bit too warm during the summer for trout.

Time of day matters, too, when you’re fly fishing on the Thunder Bay River. Most anglers find the fishing best in the morning and evenings.

Stream Flow and Current Conditions

Be sure to check the stream conditions before heading out to fish the Thunder Bay River. The USGS stream gauge near Bolton, MI provide a good indication of current conditions.

The graph below shows the stream flow (discharge) for the past 7-days. If flows are considerably above or below historical norms (yellow triangles on the chart) then fishing conditions maybe not be ideal.


  • Streamflow: 412 ft³/s
  • Gage height: 11.65 ft
Streamflow GraphGage height Graph

Best Flies for Thunder Bay River

If you’re heading out trout fishing in the spring, dry fly imitations of typical mayflies and caddis work well. Gray drakes, hex, and Isonychia are a few of the more reliable hatches.

Steelhead and large brown trout are all attracted to streamers, so having a handful available is a good idea.

However, once it turns to fall, eggs are a better choice. Any kind of salmon egg imitations are ideal for bringing in the biggest and best fish on the river.  

Here is list of general fly pattern recommendations for the Thunder Bay River:

Dry Flies

  • Yellow Sally (#12 – 16)
  • Yellow Humpy (#10 – 18)
  • Parachute Sulphur (#14 – 18)
  • Parachute Adams (#12 – 22)
  • Light Cahill (#10 – 18)
  • Elk Hair Caddis (#8 – 16)
  • Yellows Stimulator (#8 – 14)
  • Chernobyl Ant (#8 – 12)
  • Griffith’s Gnat (#16 – 24)


  • Pheasant Tail (#12 – 20)
  • BH Hare’s Ear (#12 – 20)
  • Rainbow Warrior (#14 – 22)
  • Pat’s Rubber Legs (#4 – 12)
  • Golden Stonefly (#6 – 10)
  • Tellico Nymph (#12 – 18)
  • Zebra Midge (#16 – 22)
  • WD40 (#16-20)
  • Y2K Egg (#12 – 16)


  • BH Wooly Bugger (#2 – 6)
  • Sculpzilla (#4)

Gear Recommendations

A 9-foot 5-wt fly rod and matching fly reel with floating line is perfect for fishing for trout on the Thunder Bay River. A tapered 9-foot leader, with tippet size 3X to 5X to match the flies you are throwing, is pretty standard.

You’ll want to step up to a seven- or eight-wt fly rod for smallmouth bass, steelhead, salmon and lake-run brown trout.

Thunder Bay River Fishing Report

Area fly shops, guides and websites that can provide a Thunder Bay River fly fishing report and update on current conditions are listed below:

Fishing Regulations

The state of Michigan requires that all people who are 17 years of age and older have a valid fishing license. There are resident and non-resident sport fishing licenses available.

You can purchase a Michigan state fishing license and learn about the most current regulations through the Michigan Department of Natural Resources.

Trip Planning Tips

The easiest way to access the Thunder Bay River is by plane going into Alpena County Regional Airport. You can rent a car to get around or walk and bike around the town. There are several tackle shops in the area to stock up, as well as restaurants, hotels, and campgrounds.

There are a variety of attractions to take in when you aren’t fly fishing the Thunder Bay River. The Alpena Light is right on the river and makes for a peaceful spot to spend time. Alpena Mall and the Besser Museum for Northeast Michigan are also popular locations.

Looking for more places to fish? Check out our DIY Guide to the Best Fly Fishing in Michigan