Crooked-Pickerel Lakes: Crooked and Pickerel Lakes are interconnected water bodies within the Burt Lake Watershed, together covering approximately 3,433 acres. Pickerel Lake has a surface area of 1,082 acres, a shoreline of 7.1 miles, and reaches a maximum depth of 70 feet. It is primarily fed by groundwater seepage and Cedar Creek, with Mud Creek also serving as a significant tributary. The lake supports a mesotrophic environment, characterized by moderate levels of nutrients that sustain aquatic plant growth and algae. Crooked Lake, with a surface area of 2,351 acres and a shoreline of 16.2 acres, has a maximum depth of 50 feet. The lake receives inflows from Minnehaha Creek and other smaller streams. The Crooked River serves as the primary outflow for both lakes, connecting them to Burt Lake as part of the larger Inland Waterway system. Both lakes are known for excellent fishing and the surrounding wetlands provide invaluable habitats for a variety of wildlife.

Douglas Lake: Douglas Lake is a significant feature of the Burt Lake Watershed, covering approximately 3,727 acres with a shoreline of 15 miles. The lake reaches a maximum depth of 80 feet, primarily in the deep kettle holes between Pells Island and Grapevine Point. Formed by glacial activity, Douglas Lake is a kettle lake with five deep basins, surrounded by shallow shoals that support a diverse range of aquatic plants. The lake's primary inflows are Lancaster Creek and Beavertail Creek, with water exiting via the East Branch of the Maple River, the outflow being part of the Inland Waterway. Douglas Lake is home to the University of Michigan Biological Station (UMBS), a facility for research and education in environmental sciences and field biology. UMBS's work has made Douglas Lake one of the most studied lakes globally, contributing extensive data on water quality and aquatic ecosystems.

The Sturgeon River: The Sturgeon River, one of Michigan's fastest-flowing rivers, spans 24.5 miles with a slope of nearly 15 feet per mile. It originates from two branches: the East Branch near Gaylord in Otsego County and the West Branch from Huffman Lake and Thumb Lake in Eastern Charlevoix County. These branches converge at Wolverine, from where the river flows through undeveloped forests to its mouth at Burt Lake. Celebrated for its cold-water fishing, the river sees brook trout in its headwaters and brown trout throughout most of its mainstream. The Sturgeon River's fast and clear waters also make it a favorite for paddling and tubing.

Other tributaries include: Allen Creek, Beaver Tail Creek, Beebe Creek, Berry (Cedar) Creek, Bessey Creek, Blackjack Creek, Bradley Creek, Brush Creek, Certon Creek, Club Stream, Cold Creek, Cope Creek, Crooked River, Deer Creek, Hasler Creek, Iduna Creek, Lancaster Creek, Little Carp River, Maple River, Marl Creek, McPhee Creek, Minnehaha Creek, Mossback Creek, Mud Creek (Cheboygan County), Mud Creek (Emmet County), Oden Creek, Pickerel Creek, Sanford Creek, Silver Creek, Stewart Creek, Unnamed Creek of West Burt Lake Road, Van Creek, Weber Lake, and White Goose Creek.

Other lakes include: Arnott Lake, Barhite Lake, Berry Lake, Black Lake, Bows Lake, Clifford Lake, Fitzek Lake, Fleming Lake, Fulmer Lake, Heart Lake, Hoffman Lake, Huffman Lake, Kidney Lake, Lancaster Lake, Larks Lake, Marl Lake, Munro Lake, Olund Lake, Reardon Lake, Round Lake, Sherett Lake, Silver Lake, Silver Creek Pond, Spring Lake, Standard Lake, Stewart Creek, Storey Lake, Thumb Lake, Vincent Lake, Weber Lake, Wildwood Lake, and Woodin Lake.