The greatest portion of Whitchurch–Stouffville is lies on the Oak Ridges Moraine. The moraine consists of knobby hills between 290 to 373 meters above sea level of irregularly bedded layers of unconsolidated sand and gravel (built-up glacial debris) deposited by the meltwater of the Wisconsin glacier some twenty-five thousand to ten thousand years ago. In a few cases the retreating glacier left behind and buried huge blocks of ice which, when melted, created deep, water-filled depressions known as kettle lakes. Preston Lake, Van Nostrand Lake and Musselman Lake are three such examples.
The boundaries of Whitchurch–Stouffville contain a watershed divide. Streams and rivers at the top of the Oak Ridges Moraine flow northward into the Lake Simcoe basin, part of the Lake Huron watershed. The southern sections (south of Bloomington Road) make up the headwaters of the Rouge River, and flow into the Lake Ontario basin. These headwaters include many smaller streams and creeks throughout southern Whitchurch–Stouffville. Their identification and protection, plus reforestation in these area, has been identified as urgent for rebuilding water-capacity in the Rouge River watershed which can off-set the worst environmental impacts (e.g., flash flooding, erosion and ground water contamination) of rapid urbanization. The heavily wooded Vivian Infiltration Area is an environmentally significant hydrological infiltration area that contributes groundwater to the Oak Ridges aquifer complex.
The northwestern corner of Whitchurch–Stouffville is outside the moraine and is part of the Schomberg Lake plain, an ancient lake-bed overlain by silts and fine sands. The soil formed over the former lake-bed is well-drained, arable farmland. The southern-most portion of Whitchurch–Stouffville west of Highway 48 lies below the moraine and is a clay-loam till plain.
Tree species native to Whitchurch–Stouffville include: American Mountain Ash, Balsam Fir, Bitternut Hickory, Black Cherry, Black Spruce, Bur Oak, Eastern Hemlock, Eastern White Cedar, Peachleaf Willow, Pin Cherry, Red Oak, Red Maple, Red Pine, Shagbark Hickory, Silver Maple, Sugar Maple, Tamarack, Trembling Aspen, White Birch, White Oak, White Pine and White Spruce.
Whitchurch–Stouffville has a continental climate moderated by the Great Lakes and influenced by warm, moist air masses from the south, and cold, dry air from the north. The Oak Ridges Moraine affects levels of precipitation: as air masses arrive from Lake Ontario and reach the elevated ground surface of the moraine, they rise causing precipitation.
Because of increasing greenhouse gas emissions, the Ontario Ministry of Natural Resources estimates a 1-2 degree increase both in summer and winter average temperatures in the region between 2011 and 2040, and a 0% to 10% decrease in precipitation (compared to averages between 1970 and 2000).