Multiple ice ages had a pronounced effect on the Boreal Plains. Continental glaciation flattened the landscape and left behind a variety of glacial deposits consisting almost entirely of undulating and level to gently rolling plains dotted with small lakes. Following glacial retreat 8 000 to 11 000 years ago, larger lakes developed from glacial meltwater, creating extensive deltas and dunes. Lake Winnipegosis, for example, is a remnant of the bygone Lake Agassiz.

Underlying these landforms are horizontal layers of sedimentary bedrock laid down millions of years ago during the Cretaceous and Tertiary periods.

Most of the major rivers have their origin in the Rockies. These rivers flow east across the ecozone and are the products of rainfall, snowmelt and glacial runoff at their headwaters.

The climate of the Boreal Plains Ecozone is determined by its location in the heart of North America. The Rocky Mountains to the west block moisture-bearing winds from the Pacific. The result is short, warm summers and long, cold winters. The annual precipitation, approximately 450 mm, is greater than the evaporation rate, resulting in surplus moisture of up to 100 mm near the southern edge of the ecozone and up to 300 mm in the northern and foothills regions.