Innovative and robust methods are needed to evaluate the risks to native aquatic organisms exposed to organic compounds released from contaminated sediments. In the present study, we deployed semi-permeable membrane devices (SPMDs) above sediments in a contaminated harbor at a location in the Laurentian Great Lakes (i.e. Owen Sound Bay) and prepared extracts from these passive samplers for analysis of organic contaminants and for toxicity testing using early life stages of Japanese medaka (Oryzias latipes) and lake whitefish (Coregonus clupeaformis). The concentrations of several classes of organic contaminants estimated from analysis of the SPMD extracts indicated that several polynuclear aromatic hydrocarbon (PAHs) were present in the water column in the inner harbor of Owen Sound Bay at concentrations higher than water quality standards for the protection of aquatic life. Several medaka exposed to the SPMD extract from the inner harbor as well as a positive control compound, benzo[a]pyrene, developed yolk sac edema. However, whitefish did not show the same response. Overall, these data indicate this contamination could contribute to toxicity in sensitive species. The coupling of passive sampling and in vivo bioassays with early life stages of fish shows promise as a method to assess the potential for risks from biologically available fractions of organic contaminants in water. A novel aspect of the present study is the development of a bioassay procedure with early life stages of lake whitefish involving exposures at low temperatures over durations of time that are longer than the bioassays with more conventional model fish species.