The upper section of the Saguenay Fjord was impacted by a catastrophic flood in July 1996. Contaminated sediments were capped by a layer of clean silty post-glacial sediments with background levels of trace metals and polycyclic aromatic hydrocarbons (PAHs). The capping layer was characterized by geotechnical and geochemical methods and its biological recolonization was monitored by annual sampling of the macrofauna. The strong dominance of surface deposit feeders Cirratulidae and Ampharetidae was observed at most stations in the first 2–3 years followed by carnivorous annelids such as Lumbrineridae and Nephtidae species indicating a well recolonized benthic habitat in the Baie des Ha!Ha!. The presence of benthic fauna was a major factor in modifying the density of sediments by physical mixing and irrigation, and in changing the surface roughness. The slope stability of the capping layer is considered as very good except in limited deltaic sectors at the head of the Baie des Ha!Ha! The new layer showed a good efficiency to isolate contaminated sediments from the sediment/water interface. Although manganese and iron were remobilized as the new layer became anoxic, mercury, arsenic and PAHs showed a very limited mobility through the flood layer which allowed geochemists to calculate the present fluxes of toxicants to the Baie des Ha!Ha! without interferences from older contaminated sediments trapped below the flood layer. The present flux of PAHs to bay (0.9 ng.cm-2.g-1) is about 300 times lower than the 1974 flux and 8 times lower than the 1986 flux.