The sheltered nature of Drayton Harbor, with its proximity to food sources both within the Harbor and in Semiahmoo Bay, make it a major wintering and migration staging area for aquatic birds. The extensive intertidal mudflats and shallow waters provide foraging habitat for large numbers of shorebirds and dabbling ducks. Semiahmoo Bay supports large flocks of all three scoter species; Greater Scaup; four grebe species; many duck species, including Long-tailed and Harlequin Ducks; and small numbers of alcids. Up to 650 loons have been counted here in a single day. Five surveys conducted throughout one winter in Drayton Harbor each showed a total of more than 15,000 birds. The highest recorded counts of Red-necked Grebes (98) and Horned Grebes (382) on the Washington coast occurred in this census.
The increasing popularity of Drayton Harbor as a recreational area jeopardizes its value as a winter foraging site for birds. The primary threat is disturbance from boating and other recreational activities. Expansion of two marinas in the vicinity of the channel has resulted in dredging and filling, and alteration of the natural shoreline. Residential development has removed or altered much of the natural vegetation on the shorelines, and this trend is continuing. Some shellfish beds on the west side of Semiahmoo Spit are polluted, presumably from runoff and failing septic systems. Introduction of non-native marine flora and fauna is also a concern.