McDonald Creek originates in the high country of Glacier National Park, flowing from the Continental Divide westward through a glacially-carved valley before draining into Lake McDonald, the park's largest lake. From the lake's outlet near Apgar, the creek continues approximately 2.5 miles before joining the Middle Fork Flathead River near West Glacier. This cold, clear waterway exemplifies the pristine character of Glacier's aquatic ecosystems, with its crystalline waters fed by snowmelt and glacial runoff throughout much of the year.

The creek's paddling character varies dramatically by season and location. Above Lake McDonald, the upper reaches flow through remote wilderness with limited access, while the section from Lake McDonald to the Middle Fork confluence offers more accessible paddling opportunities. The outlet area near Apgar provides a gentle float suitable for beginners, particularly from mid-summer through early fall when water levels moderate. This lower section meanders through forested bottomlands with occasional riffles but no significant whitewater, making it appropriate for kayaks, canoes, and stand-up paddleboards.

Peak paddling season runs from late June through September, after spring runoff subsides but before autumn's declining water levels. Early season conditions can be challenging due to cold water temperatures and higher flows, while late summer offers warmer conditions and clearer water visibility. The creek's glacial origins mean water temperatures remain frigid even in summer, necessitating appropriate safety precautions.

The riparian corridor supports dense coniferous forests dominated by western red cedar, Douglas-fir, and western hemlock. Wildlife sightings frequently include white-tailed deer, black bears, and various waterfowl. The creek maintains populations of native westslope cutthroat trout and bull trout, both species of conservation concern. Harlequin ducks nest along the upper reaches, prompting seasonal paddling restrictions between Mineral Creek and Lake McDonald from April through September.

Notable landmarks include the historic Lake McDonald Lodge, built in 1914, and the confluence area where McDonald Creek meets the Middle Fork Flathead River. The Going-to-the-Sun Road parallels portions of the creek, providing scenic overlooks and access points.

Primary access is from Apgar Village at the foot of Lake McDonald, located approximately 2 miles from West Glacier. The area lies within Glacier National Park boundaries, requiring park entrance fees and adherence to National Park Service regulations. Paddlers must practice Leave No Trace principles and remain aware that this is active grizzly bear habitat. The creek's location within a designated Wild and Scenic River corridor means motorized watercraft are prohibited, preserving the area's natural character for human-powered recreation.