We examined factors and pathways involved in the transfer of mercury (Hg) to the food web in St. Lawrence River embayments near Cornwall, Ontario, where natural remediation of contaminated sediments (eventual burial by settling of cleaner sediments) has been adopted as a management strategy. Yellow perch (Perca flavescens) from one of the study zones (Zone 1) along the river by Cornwall contained significantly higher total mercury (THg) concentrations than perch from other equally contaminated zones. While THg concentrations in benthic invertebrates did not vary among contaminated zones, THg concentrations in yellow perch and invertebrate prey recovered from the perch stomachs were 1.5-2.5 times higher in Zone 1 than those from other zones, suggesting that prey selection affects THg accumulation more than habitat location. No significant differences were found in THg concentrations among different prey species within Zone 1, although there were significant differences in THg concentrations in the same prey species within Zone 1. In contrast, THg concentrations among different prey species increased significantly with trophic level in other contaminated and reference zones. The lack of correspondence between trophic position and THg accumulation in Zone 1 suggests two possibilities: (1) yellow perch in Zone 1 are highly mobile and are assimilating THg from a wide range of prey across Zone 1 with variable THg concentrations and (2) there may be an important non-dietary source of THg to the Zone 1 food web. Potential waterborne Hg sources to Zone 1 were investigated. Whereas THg and MeHg values in discharges from a disused canal were similar to Zone 1 surface water values (0.97 and 0.04 ng l -1 , respectively), concentrations in storm sewer and combined sewer overflows discharging in the vicinity of Zone 1 were 19-45-fold (THg) and 2-4-fold (MeHg) higher than upstream river water. Contributions of Hg to the water column from sediment-water diffusion, estimated using a simple, well-mixed reactor model, ranged 0.05-0.1% of the surface water THg concentration and 1-2% of the MeHg concentration measured in summer months in Zone 1. Although not investigated in the other zones, a strong correlation (r 2 = 0.82) was found between Guest editors: M. Power, J.