The headwaters of Green Cove Creek emanate from a large intact wetland complex largely protected by conservation easements, acquisitions, and a City of Olympia . The riparian corridor is comprised of mixed conifer and deciduous forest with only a few sites warranting improvement. Because it is relatively intact, Green Cove Creek is Olympia's priority for salmon habitat protection measure.

The Green Cove Creek Comprehensive Drainage Basin Plan (1998) recommended minimum canopy cover of 60% within the watershed to prevent excessive stormwater impacts. The City of Olympia has downzoned the upper Basin and instituted more stringent development standards to maintain the forest cover and protect the creek. Although the City has instituted these standards, significant residential development pressures exist in this desirable area, especially new home construction. Tidal influence occurs in the estuary and at the mouth of the creek, allowing for a fresh and saltwater mixing despite the presence of some bulkheads. Green Cove has two fishways assessed by WDFW; one has retrofitted baffles which impact upstream adult and juvenile migration while the other is passing fish.

The southern portion of the basin lies within the City of Olympia and the Urban Growth Area. The headwater wetlands lie within the city's Grass Lake Park. The Capitol Land Trust has protected some additional wetlands and forested uplands in the upper basin. The majority of the basin lies within private ownership characterized by residential land uses.

Description from the Salmon Habitat Protection and Restoration Plan for Water Resource Inventory Area 13, Deschutes. For more information see the previously stated document or the Salmon Habitat Limiting Factors Final Report Water Resource Inventory Area 13