East of Ludington near Baldwin, the Pere Marquette River is popular for trout fishing, but is probably more well-known for its steelhead and salmon runs. The brown trout and rainbow trout are there all year round waiting for you, but the steelhead run from September to March and the Chinook run from August to October.
The headwaters start at the confluence of the Little South and the Middle Branch (which has excellent fly fishing, too) near Marlborough. The river heads west for about 30 miles and then drains into Lake Michigan near Ludington. The first 8 miles are designated artificial-fly / catch-and-release from SR37 to Gleasons Landing. In this stretch, you can expect to find the typical riffles, runs and pools which are home to large trout and steelhead.
The lower section of the Pere Marquette River for fly fishing is from Gleasons Landing to Lake Michigan is also an excellent fishery. You could catch a 15 pound steelhead if you are lucky. The river has a lot more volume and is much deeper, so you may want to float.
Overall, Pere Marquette River is the 14th most popular fly fishing river of all 26 fly fishing spots in Michigan.