First and foremost, have you locked in a specific portion of September yet? If not,
I would urge you in the strongest possible terms to visit Glacier during the last week-ten days of September. The last half of September and first week of October are a truly magical time of year to head for the high country. With school back in session, visitation is low and services will be limited, but you will seemingly have the park and, particularly, the backcountry all to yourself. If the weather is accommodating, crisp, cool days and brilliant, blue skies are the norm. Most importantly, you will have the opportunity to witness the daily transformation of the aspen as they assume their electrifying cloaks of yellow, orange and red. If you are supremely fortunate, a recent dusting of the peaks will add the final artistic touch to these magnificent landscapes. It is also the beginning of the fall rut for many big game species, so chances are excellent that you will hear elk bugling in the canyons, a signature sound of wilderness that you will never forget.
As for must-see attractions, the remote Kintla Lake area in the extreme northwest corner of the park, the Two Medicine valley in the southeastern sector, the Many Glacier area, which is somewhat reminiscent of the Swiss Alps (see
Many Glacier Hotel | Glacier National Park | US Park Lodging and
Grinnell Lake Photos & Framed Prints by James Kay Photography, Glacier National Park), and the Chief Mountain area (see
Chief Mountain Photo - Glacier Park Photo Gallery), both of which are in the northeastern corner of the park all fall in this category. You certainly will want to traverse the Going-to-the-Sun Highway in its entirety and September 21st is the last day you will be able to do so.
I will discuss each of these areas in order, but first want to address St. Mary Lake as well as fall foliage destinations. The truly iconic view of Glacier is from the Wild Goose Island overlook (see
Framed Prints Saint Mary Lake Photos by James Kay Photography - Glacier National Park) near the shores of St. Mary Lake, but this vantage point is only 7.6 miles from the eastern terminus of the Going-to-the-Sun Highway, so you will need to be there by September 21st. You will find it well worth the effort to target the St. Mary area during this time since the aspen groves which border this lake typically put on a superb show. Incidentally, the finest accommodation in this portion of the park is the St. Mary Lodge and Resort (
Glacier Park Inc.). If you want something cheaper and more rustic, the St. Mary KOA Campground is about 1-2 miles from there (
St. Mary / East Glacier KOA | Camping in Montana | KOA Campgrounds). And, yes, they do have camper cabins. We have had the pleasure of being serenaded by elk while staying at that facility.
As for fall foliage in general terms, Glacier puts on a magnificent display but hotspots are more widely distributed than in Colorado, where entire mountainsides are carpeted with aspen. Larch, a deciduous conifer (yes, you read that correctly) can be found on the shores of lakes located in the western half of the park, particularly those close to the North Fork of the Flathead, but they do not typically turn color until later in October. The most magnificent stands of aspen are, for the most part, located on the drier, more windswept eastern side of the park, particularly the St. Mary lake area, Many Glacier and Two Medicine valleys, and the Chief Mountain area. If you bring your passports, the adjoining Waterton Lakes National Park is also worth visiting (
Waterton Lakes National Park - Home Page). The Prince of Wales Hotel (
Glacier Park Inc.: Prince of Wales Hotel), an absolutely stately facility, is located there.