- Sizeable eelgrass beds are present in the lagoon, covering 15 hectares, or 19% of the total subtidal area. Eelgrass is a flowering plant with grass-like blades that hosts a complex marine food web. It provides habitat for fish and invertebrates, and food for Brant Geese.
- Kelp, principally Laminaria saccharina, grows in areas of the lagoon that receive the strongest tidal currents, at the entrance to the lagoon and in the northeastern portion. Kelp covers six hectares of the lagoon.
- Green algae, principally Ulva or sea lettuce and Enteromorpha, grow among eelgrass and kelp, and cover 28 hectares or 34% of the subtidal area.
- Historically, several of the creeks that flow into Esquimalt Lagoon supported Pacific salmon and cutthroat trout spawning, but the creeks have been degraded by pollution, alteration of the stream flows and channel modification. Today, very limited numbers of salmon are known to spawn in Colwood Creek. Resident cutthroat trout live in Colwood Creek and Bee Creek, but it is not known if sea-run cutthroat still spawn in any of the creeks.
- Pacific herring were known to spawn in Esquimalt Lagoon before the 1950s, and spawning was observed in the early 1990s. Herring is an important food source for many marine fish, mammals and birds.
- Among the intertidal gravel bars at the entrance to the lagoon, butter clams, littleneck clams, mussels and oysters are quite plentiful. These are likely the largest and most significant intertidal clam beds in the area of Victoria and Esquimalt Harbours. As noted previously, First Nations historically used Esquimalt Lagoon for harvesting shellfish, but today shellfish harvesting is prohibited due to contamination.
Esquimalt Lagoon is one of the most important bird feeding areas in the CRD harbours, and is classified as a federal Migratory Bird Sanctuary. Large numbers of seabirds, shorebirds, waterfowl can be found here year-round, particularly around the gravel bars at the northeast end. Some species are migratory and use the lagoon to fuel up for their long journeys. Unfortunately, mute swans and domestic geese also live and feed in the lagoon. These invasive species have been introduced by people and compete for food and habitat by bullying native birds with aggressive behaviour.
Some commonly sighted waterfowl and sea/shore birds include members of the following groups:
- Diving ducks, mergansers and coots such as bufflehead, canvasback, red-breasted merganser, common goldeneye, lesser scaup
- Gulls and terns including glaucous-winged gull; mew gull and California gull
- Shorebirds including dunlin, greater yellowlegs, black oystercatcher, black turnstone, killdeer and western sandpiper
- Swans, geese and dabbling ducks including mallard, Canada goose, American widgeon, northern pintail
- Double-crested cormorants
- Great blue herons
The types of birds found in the lagoon change seasonally as different migratory species arrive and depart, and resident species move around in the local area. During the winter and early spring, diving ducks, mergansers and coots
are one of the most plentiful groups, as species such as bufflehead migrate from inland breeding areas to winter on the coast. During the summer and fall, gulls and terns
dominate the area, particularly when California gulls migrate to the coast from their northern prairie breeding grounds. The ubiquitous glaucous-winged gull is the most common gull throughout the year in this area. Mallards and Canada geese are also resident birds, although their numbers increase when migrating populations pass through during spring and fall.
Other land-based bird species that live and/or feed near the lagoon include crows, ravens, bald eagles, ospreys, hawks, swallows, great horned owl, belted kingfisher and woodpeckers.