The mouth of Skookum Creek is home to a well-developed estuary characterized by estuarine emergent wetlands with deep pools that provide quality habitat for juvenile salmonids. About 74 acres of this area are protected within a Natural Area Preserve managed by the Washington Department of Natural Resources (Taylor et al. 1999).
Sampling by the Thurston County Health Department in 1984-85 found no exceedances of Class A Marine criteria for fecal coliform. However, four out of five freshwater stations exceeded Class A standards. Kennedy Creek met the freshwater standards.

Sampling by the Thurston County Health Department in 1984-85 found no exceedances of Class A Marine criteria for fecal coliform. However, four out of five freshwater stations exceeded Class A standards. Kennedy Creek met the freshwater standards. Schneider Creek, Cleeves Creek, and Burns Creek all exceeded Class A fecal coliform standards. Livestock appeared to be the source of contamination. A study by Mason County Health Department found that the major sources of freshwater to Little Skookum Inlet failed to meet Class A fecal coliform standards. However, marine water quality was only impacted during rainfall when bacterial loading increased substantially. There are at least 30 private docks on Little Skookum Inlet and over 170 on Totten Inlet (Soil Conservation Service et al. 1988). No quantitative habitat inventories are known to have occurred in this area.

Description from the Salmonid Habitat Limiting Factors Water Resource Inventory Area 14, Kennedy-Goldsborough Basin. For more information on Totten and Little Skookum Inlet's nearshore habitat see the Level 1 Project Totten / Little Skookum Inlet or the previously stated document.