The more wave-exposed rocky outcrops near the harbour mouth support dense kelp beds dominated by sugar kelp (Laminaria saccharina
) and five-rib kelp (Costaria costata
). A diverse understory of other algae and invertebrates such as sea urchins form part of this dynamic ecosystem. Dense but less diverse kelp beds occur around Smart and McCarthy Islands and along the shoreline between Yew Point and Rodd Point. Canopy forming kelp beds are rare, but a small bed of bull kelp is located on Whale Rock, the largest subtidal rock outcrop in the harbour.
Esquimalt Harbour today has very little eelgrass, only about 0.5 ha spread out over several small locations. Probably these were much more extensive prior to the industrial activity in the harbour, as the depositional sediments through much of the harbour would have been suitable substrate for eelgrass to thrive in. Dredging, log booming and infilling of the foreshore has undoubtedly had a major impact on eelgrass distribution and survival. As eelgrass provides critical habitat for juvenile fish such as salmon and herring, as well as a multitude of other forms of marine life, it is vital to protect and enhance the few remaining pockets that persist here. Eelgrass is also important for controlling erosion, as it traps and holds sediments in the marine and estuarine environments.
High current areas
Unlike Victoria Harbour and the Gorge Waterway, Esquimalt Harbour does not have many areas of high currents, adding high ecological value to the few that do occur there. Paddy Passage and the channel between Smart and McCarthy Islands are two such high current areas, where sessile filter-feeding assemblages of sponges, tube worms and bryozoans are common.
Estuaries and mudflats
The main estuary in Esquimalt Harbour is at the mouth of Millstream Creek
. The extensive mudflats here are home to a variety of intertidal clams that once were an important food source for First Nations people of the area. The harbour is currently closed for clam harvesting due to fecal coliform contamination.
The Millstream Creek estuary and mudflat is an important feeding area for birds, providing a valuable source of worms, shellfish and other mudflat-dwelling organisms.