Salt Creek enters saltwater on the east end of the Central Strait of Juan de Fuca. Sedimentation is a problem in Salt Creek, and is likely the result of heavy logging adjacent to west side tributaries in the 1980s. A few areas of Salt Creek have high LWD loadings, but upstream of RM 2 there is a particular lack of large wood. This area is also channelized and incised. The Camp Hayden Road is a riparian road constructed in the floodplain along the mainstem from RM 1-2. A private road cuts across the estuary, and prevents the lateral migration of Salt Creek, disconnecting it from potential wetlands and the tidally-influenced reaches of the creek, with an adverse impact to salmonid habitat. About 15 acres of tidal marsh have been lost to the road. Animal grazing along some of the banks could decrease water quality, as well as increase erosion. In addition, water quality issues for the Salt Creek/Crescent Bay area include residential runoff. Crescent Bay is comprised of an extensive eelgrass bed within the main bay, and lush diverse kelp beds fringing Tongue Point and extending west to Agate Point. The shallow eelgrass is important for sand lance and juvenile salmon, and the kelp is also important for salmon habitat. Major factors limiting salmon habitat in Salt Creek are lack of LWD, land conversion, loss of wetlands and salt marsh, and increased culverts, riparian degradation and stormwater.
Salt Creek and its tributaries provide important coho salmon spawning and rearing habitat throughout the mainstem and tributaries downstream of a passable dam at RM 6.5. The creek used to support chum, now existing at very low levels. Chinook have not been documented there in recent years, and winter steel-head are declining. Lack of LWD impacts salmonid habitat by allowing the channel to be-come destabilized, with a lack of pools and shade. The high value salt marsh and estuarine habitat provide important rearing and holding for salmon entering and leaving the stream, as well as for sand lance. Land conversion impacts riparian habitat, increases sedimentation and creates habitat loss in the watershed.