Morningside Park is home to the largest remaining forest block within the Highland Creek watershed. As such, it provides high-quality habitat for many wild creatures and functions as a migration corridor for wildlife within an intensely urbanized region. The park has been recognized for its ecological significance and is now part of the City's natural heritage system. To protect and enhance the ecological integrity of Morningside Park, the City of Toronto has undertaken native tree and shrub plantings at this site.
As it runs through Morningside Park, Highland Creek is surrounded by steep valley slopes up to 30 metres high. In some areas, these slopes are unstable and are susceptible to erosion due to the composition of the soil.
Shortly after World War II, the valley surrounding Highland Creek was inhabited by people affected by a housing shortage. These residents were regularly under threat from flash floods and erosion near their dwellings. In 1954, Hurricane Hazel hit Toronto and caused severe city-wide flooding. This event led to floodplain land in the Toronto region being acquired by public agencies and the Highland Creek valley has not been inhabited since then.