The growth of Toronto brought serious ecological problems to Whitchurch-Stouffville. Between 1962 and 1969, hundreds of thousands of litres per month of sulfuric acid, calcium hydroxide, and oil waste were poured into unlined Whitchurch-Stouffville dumps never designed as landfill sites and situated directly above the town's main aquifer.
The most significant challenge facing Whitchurch-Stouffville in the coming years, however, is the federal government's proposed development of an international airport immediately south-east of Whitchurch-Stouffville (the Pickering Airport lands).