The complex geology of the region includes a remarkable diversity of formations and landforms. Within the granite-dominated landscape distinct rock formations lie scattered: folded gneiss dots Mulcaster Island; Gordon Island is underlain by sandstone, visible in shoreline bluffs; limestone beaches surround Cedar Island. Throughout the region, unique landforms add diversity to the topography: Grenadier and Hill Islands are large, narrow eskers; the whaleback shape of Mermaid Island was formed by glacial polishing and scour; potholes were literally dug out of the rock on Bostwick Island; the polished northeast facing slopes and jagged western facing cliffs clearly show the direction of glacial movement.

The Frontenac Arch is a narrow granite spur of the Canadian Shield that bisects the region and provides the rugged character for which the Thousand Islands are renowned. The continental landform is ecologically significant due to connectivity it provides, joining the northern forest of the Algonquin Highlands and the rugged Adirondack Mountains. Although the waters of the Great Lakes can be a barrier to migrating flora and fauna, the St. Lawrence River funnels the water into a narrow channel here, and the islands form stepping stones shortening distances across the river. Thus, the Axis provides a corridor for wildlife movement that maintains the integrity of the region and the wild regions to the north and south.

The Frontenac Axis stands wild today because its rugged topography of rock and wetlands made much of the region poor farmland for early settlers and held only scattered pockets of large forests for timber barons. The region remains wild thanks to caring stewardship initiatives undertaken by the active conservation community that includes federal, provincial and municipal agencies working in concert with local partners such as land trusts and landowners associations.

The Thousand Islands is a remarkably biodiverse region that hosts a rich and complex ecology characterized by thick woods, rocky outcrops and river marshes. Mature mixed forests of hemlock, white pine, pitch pine, red and white oak, maple and birch fill the forests with vibrant life. The region is a tension zone" of rapid transition between northern and southern forest that supports plants and animals from several different geographic regions.

The Thousand Islands ecology is strongly affected by several inter-related factors that combine to create a richly diverse ecoregion. As the confluence of east-west and north-south wildlife movement corridors, species characteristic of several forest zones inhabit the Thousand Islands. Some forest communities are favoured, while others are hindered, by the acidic soils of the granitic bedrock that contrast sharply with the alkaline soils associated with neighbouring lowlands. The dominant east-west orientation of the islands creates a distinct north aspect and south aspect on larger islands. This creates unique microclimates - or slight differences in temperature and moisture - which provide subtle habitat variations for wildlife to carve a niche. Finally, the presence of Lake Ontario immediately adjacent to the region has the effect of a 'heat sink'; it moderates the local climate of the Thousand Islands. Notable examples of species which are common in the region, but rare in the rest of Canada include: Rue Anemone; the Black Rat Snake, Canada's largest snake; Pitch Pine, a southern species whose range extends along the Frontenac Arch to just north of the 1000 Islands; the Least Bittern, a wading bird whose wetland habitats are decreasing elsewhere within its northern range; and a small population of deerberry that remains on some islands in the area.