Many species of wildlife are seen regularly in the Gorge Waterway and Portage Inlet, including harbour seals, river otters, raccoons, the occasional mink and many birds. The whole inlet is part of a Migratory Bird Sanctuary, and provides important habitat and feeding grounds for thousands of birds either seasonally or year-round.
The native Olympia Oyster (Ostrea lurida) is an important species found in the Gorge and Portage Inlet. Historically, this oyster was an important food source for First Nations and early European settlers in the region. Oysters are filter feeders that help to clear the water of sediment and organic matter, and provide an important food source for other invertebrates, birds and other wildlife.
Pacific herring once spawned regularly in the upper Gorge, primarily in the eelgrass beds. This has not been observed since the 1970s, but schools of herring still enter the Gorge annually. People often jig for herring from the Craigflower Bridge and Selkirk Trestle in the early spring.
Spawning populations of coho and chum salmon as well as cutthroat trout occur in Craigflower and Colquitz creeks, both of which flow into Portage Inlet. Although the runs are much reduced from historic times, there are ongoing efforts to restore these populations. Juvenile fish of many species shelter in the abundant eelgrass beds in the Gorge and Portage Inlet.