This area of Algonquin Park is characterized by shallow stony sand till over ridges and knobs of Precambrian rock. In Algonquin Park, the bedrock and overburden are generally granitic with very low base content. The Swan Lake Forest Research Reserve encompasses a variety of site conditions, ranging from deep-soiled drumlinoid deposits of moulded silty sand till to uniform valley trains and outwash flats of sand and gravel.
Scott Lake lies immediately to the east of a prominent drumlinoid, the lower reaches of which form the western shore of the lake. Soils of the drumlin vary from well-drained loamy sands and sandy loam brunisols with a rich soil profile at the top to moderately rich podsols with a thin A horizon over a weak iron-humus B and some mottling at the bottom. Scott Lake, at an elevation of 475 m a.s.l., is characterized by annual means of 100 frost free days and 86 to 91 cm of precipitation and lies in the B3 wet humid moisture region of the province.
The lake is bordered by a conifer ring which consists primarily of eastern hemlock (Tsuga canadensis (L.) Carr.) along with eastern white cedar (Thuja occidentalis L.), white pine (Pinus strobus L.), and balsam fir (Abies balsamea (L.) Mill.). While the ring around the lake is predominantly coniferous, some yellow birch (Betula alleghaniensis Britt.) and red maple (Acer rubrum L.) trees do occur near the shoreline. Bordering this coniferous ring is a deciduous matrix composed primarily of sugar maple (Acer saccharum Marsh.), American beech (Fagus grandifolia Ehrh.) and yellow birch. Shrubs characteristic of wet areas predominate at the water's edge, primarily leatherleaf (Chamaedaphne calyculata (L.) Moench), sweetgale (Myrica gale L.), and Labrador tea (Ledum groenlandicum Oeder). Pipewort (Eriocaulon septangulare With.), water lobelia (Lobelia dortmanna L.), and white water lilies (Nymphaea odorata Ait.) are the most common species of aquatic vegetation, although aquatic macrophytes are quite sparse in Scott Lake.