Depending on exactly where in the Flathead Lake area you will be staying and how much time you want to devote to “exploring its shores,” one area that you might consider is the National Bison Range near Charlo, MT. Flathead is an enormous lake and, from Kalispell to Polson, at its extreme southwestern corner, comprises a 51-mile drive. From there, “take Highway 93 south of Polson for 18 miles to State Highway 212; travel 12 miles to the entrance” of the Bison Range (
https://www.fws.gov/refuge/National_Bison_Range/Plan_Your_Visit/directions.html). So, that would be roughly an 81-mile drive one way, which may well be more than you want to divert your itinerary.
With respect to lakes, you will skirt the shores of Lake McDonald and St. Mary Lake, as well as McDonald Creek, for many miles as you traverse the Going-to-the-Sun Road. The Wild Goose Island pull-off, which overlooks St. Mary Lake is, in my opinion, the signature vista of Glacier NP. Lower Saint Mary Lake is actually on the Blackfeet Reservation, but is absolutely gorgeous in fall, due to the heavy aspen concentrations along its shores. Then, you have Lake Sherburne, which extends up much of the Many Glacier valley’s length, and Swiftcurrent Lake, which is right next to the Many Glacier Hotel. In the Two Medicine valley, you have Lower Two Medicine Lake, which straddles the park/reservation boundary, and Two Medicine Lake, the shores of which abut the terminus of the road into this valley.
Should you decide to take the southern route (US2) around Glacier, you will follow the Middle Fork of the Flathead River for a significant distance east from West Glacier. If you take the combined route of Camas Creek Road and the Outer, then Inner North Fork Road, north from Apgar, you will be rewarded with views of the wild North Fork of the Flathead region and, finally, Kintla Lake, which provides a fitting punctuation mark to your exploration of that area. See this website (
http://www.enjoyyourparks.com/GlacierParkNorthForkArea.html) for an overview of the North Fork area and this page (
https://www.nps.gov/glac/planyourvisit/maps.htm) for a good map of the entire park.
As for waterfalls, consult this chart (
http://www.hikinginglacier.com/hiking-glacier-national-park.htm) with respect to the relative difficulty of trails in the park. According to it, the Running Eagle Falls, Baring Falls, Trail of the Cedars, and St. Mary Falls trails are among the shortest and least challenging trails in Glacier. Trailheads for the Baring Falls and St. Mary Falls trails are directly accessible from the Going-To-The-Sun Road, approximately 10 miles west of the St. Mary Entrance Station. The trailhead for Running Eagle Falls is located 1.1 miles west of the Two Medicine entrance station.
The Trail of the Cedars, one of two wheelchair-accessible trails in Glacier National Park, is a loop hike that begins and ends on the Going-To-The-Sun Road, located 5.5 miles east of the Lake McDonald Lodge. Since "this is an extremely popular trailhead, parking can be a [problem] during peak travel season. Being situated on the eastern edge of the maritime climate of the Pacific Northwest, the Lake McDonald Valley also marks the extreme eastern limits for western hemlocks and red cedars. The humidity in this valley allows the cedars to grow to heights of 100 feet, and diameters of 4 to 7 feet. Some of the trees in this area are estimated to be more than 500 years old.” In short, this is a tiny little pocket of the Pacific Northwest coast, both climatically and botanically. See
https://www.jameskay.com/landscape-...tana.html#NP=608715bfd1456ba659bed5806e812b56 and
http://www.hikinginglacier.com/trail-of-the-cedars.htm. If you choose to take the spur trail to Avalanche Lake, your journey will become a bit more challenging, but you ultimately will be rewarded with views of, first, Avalanche Creek, which provides a brilliant contrast between the clarity of its water and the lushness of surrounding vegetation (see
https://www.jameskay.com/landscape-...tana.html#NP=608715bfd1456ba659bed5806e812b56), and, then Avalanche Lake, which is fed by no less than five waterfalls.
Obviously, Logan Pass, which is located on the Continental Divide, deserves an extended stop on your way across the Going-To-The-Sun Road. A visitor center is located there, and the Hidden Lake (
https://www.jameskay.com/landscape-...tana.html#NP=608715bfd1456ba659bed5806e812b56) and Highline Trails begin there. Among the multitude of magnificent peaks in Glacier, two deserve special notice. Mount Gould is the striking peak that gives the Many Glacier valley its Switzerland-like feel. Chief Mountain, located in the extreme northeastern part of the park, stands like a lone sentinel looking out over the Northern Plains; it remains highly sacred to the Blackfeet.
