The Good Harbor Bay Trail is almost entirely flat with just a few small grades. Near the beginning of the trail, there is a short section of low coastal dunes, where there is access to the beach. Then the trail turns away from Lake Michigan and becomes wooded for the remainder of its length. A portion of the trail passes through a swamp, and a small bridge assists in crossing a couple of wet spots.

The trail lies between Little Traverse Lake and Lake Michigan. This entire strip of land was underwater at the end of the Ice Age and has emerged gradually during post-glacial times. Along this trail, you can see the different plant communities that have developed in zones parallel to the shoreline. Starting from the beach and traveling inland, you pass through an active dune zone, a shrub zone, a pine-oak forest, and the beginnings of a beech-maple forest. Just a few thousand years ago, the forested zones were barren beaches. Plants, through their growth and decay, have built up a topsoil on top of old dunes.