The flora there include many of the same plants found on the mountain, with the exception of some of the more sensitive species, and with the addition of some exotics that have presumably escaped from residential properties along the upper edge.

Below the highway, Eagle Creek runs through Charles Rummel Park, and then once again enters a residential zone, where it is mostly channelized, and occasionally culverted.

The protected lands of Burnaby Mountain, as well as the lands of Burnaby Lake Regional Park are forested with a second growth forest that primarily consists of bigleaf maple, red alder, western hemlock, western redcedar, and Douglas-fir, with an underbrush of salmonberry, Indian plum, red elderberry, and other shrubs and herbs.

In areas which have been converted by residential development, exotic and invasive species predominate, including English ivy and Himalayan blackberry.

Eagle Creek has experienced a number of spills in residential areas that caused serious damage to the trout and salmon population, most recently in the summer of 2006.