Spatial and temporal changes in mercury (Hg) concentrations and organic carbon in lake sediments were examined from the Hudson Bay Lowlands to investigate whether Hg deposition to sediments is related to indicators of autochthonous production. Total organic carbon, "S2" carbon (mainly algal-derived OC), C:N and ∂13C indicators suggest an increase in autochthonous productivity in recent decades. Up-core profiles of S2 concentrations and fluxes were significantly correlated with Hg suggesting that varying algal matter scavenging of Hg from the water column may play an important role in the temporal profiles of Hg throughout the sediment cores. Absence of significant relationship between total Hg and methyl Hg (MeHg) in surficial sediments suggested that inorganic Hg supply does not limit MeHg production. MeHg and OC were highly correlated across lakes in surface and deep sediment layers, indicating that sediment organic matter content explains part of the spatial variation in MeHg concentrations between lakes. © 2012 Elsevier Ltd. All rights reserved.