This study characterises the sediment dredged from a lagooning system composed of a settling pond and three lagoons that receive leachates from a municipal solid waste (MSW) landfill in France. Organic carbon, carbonate, iron oxyhydroxides, copper (Cu) and zinc (Zn) concentrations were measured in the sediment collected from upstream to downstream in the lagooning system. In order to complete our investigation of sedimentation mechanisms, leachates were sampled in both dry (spring) and wet (winter) seasonal conditions. Precipitation of calcite and amorphous Fe-oxyhydroxides and sedimentation of organic matter occurred in the settling pond. Since different distributions of Zn and Cu concentrations are measured in sediment samples collected downstream in the lagooning system, it is suggested that these elements were not distributed in a similar way in the leachate fractions during the first stage of treatment in the settling pond, so that their sedimentation dynamics in the lagooning system differ. In the lagoons, it was found that organic carbon plays a major role in Cu and Zn mobility and trapping. The presence of macrophytes along the edges provided an input of organic matter that enhanced Cu and Zn scavenging. This edge effect resulted in a two-fold increase in Cu and Zn concentrations in the sediment deposited near the banks of the lagoons, thus confirming the importance of vegetation for the retention of Cu and Zn in lagooning systems.