Lake McDonald is approximately 10 miles (16 km) long, and over a mile (1.6 km) wide and 472 feet (130 m) deep, filling a valley formed by a combination of erosion and glacial activity. Lake McDonald lies at an elevation of 3,153 feet (960 m) and is on the west side of the Continental Divide. The Going-to-the-Sun Road parallels the lake along its southern shoreline. The surface area of the lake is 6,823 acres (27.6 km²).
The lake is surrounded by a dense coniferous forest dominated by various species of spruce, fir, and larch. At the westernmost section of the lake in Apgar there is a National Park Service visitor center, limited lodging and dining facilities as well as outboard powerboats available for rental. Lake McDonald Lodge is the largest lodging facility on the lake and is approximately 5 miles (8 km) east along the Going-to-the-Sun Road. McDonald Creek flows into and drains from the lake, and empties into the Middle Fork Flathead River shortly after.