A baseline environmental characterization of the northeastern reaches of Bristol Bay, Alaska was conducted using the National Status and Trends’ sediment quality triad approach. The study area was subdivided into 6 strata based on geophysical and hydrodynamic patterns (the upper and lower reaches of Nushagak and Kvichak Bays, Dillingham Harbor and the mouth of the Naknek River). Within each stratum, a stratified random sampling approach was used to select sampling sites for infauna and sediment chemistry. Ambient toxicity was assessed at a subset of sites using two bioassays (Microtox® and sea urchin fertilization and development). Fish species including, starry flounder (Platichthys stellatus) and rainbow smelt (Osmerus mordax) were collected by trawl for body burden analyses for chemical contaminants. Persistent organic pollutant concentrations were low relative to National Oceanic and Atmospheric Administration (NOAA) sediment quality guidelines (SQG). All metal/metalloid concentrations were below NOAA SQGs except for arsenic which was uniformly above the threshold SQG. Benthic communities were relatively sparse at most locations due to harsh physical oceanographic conditions. Significant chemical toxicity was virtually absent except for selected locations with high pore-water ammonia levels associated with fish processing plant waste streams. Contaminant body burdens were very low in the fish tested. The fish were generally healthy and non-contaminated.