Lake Winnipesaukee is a classic glacially formed oligotrophic (this means low fertility) lake. The water is quite clear; average main lake and bay visibility is 27-29 feet. Visibility is slightly less in central portions of Moultonborough Bay (21 feet) and less still in the extreme northern end of this bay (less than 15 feet).
The physical nature of the main-lake shoreline ranges from boulder-strewn to sandy. Some back-bay areas (e.g. the extreme northern end of Moultonborough Bay) have wetland shorelines, but this habitat is limited overall. The lake bottom and reefs/shoals are predominantly ledge, boulders, cobble, gravel, and sand, with softer muck bottoms in basin and back-bay areas.
Emergent and submergent vegetation are sparsely located throughout the lake. Submergents include pondweed, variable milfoil, bladderwort, quillwort, and pipewort; emergents include yellow and white water lily, pickerelweed, and water shield. The greatest concentrations of these aquatics are found in the northern end of Moultonborough Bay.