A baseline environmental characterization of the embayments and fjords on the Kenai Peninsula, Alaska was conducted using a sediment quality approach based on sediment chemistry, and benthic invertebrate community structure. Sediment toxicity and resident fish body burdens were also assessed at one bay near an abandoned mine site. The study area was subdivided into seven distinct water bodies on the peninsula’s north side, draining into Kachemak Bay, and two on the western tip of the peninsula, opening into Lower Cook Inlet. Sampling sites for water quality measurements, sediment, and benthic infauna were randomized within each embayment. Concentrations of 140 organic and elemental contaminants were analyzed. Habitat parameters (depth, salinity, temperature, dissolved oxygen, sediment grain size, and organic carbon content) that influence species and contaminant distribution were also measured at each sampling site. A detailed benthic community condition assessment was performed at each site.