The contamination of drinking water resources by toxic metals is a major problem in many parts of the world, particularly in dense populated areas of developing countries that lack wastewater treatment facilities. The present study characterizes the recent evolution with time of some contaminants deposited in the Congo River and Lake Ma Vallée, both located in the vicinity of the large city of Kinshasa, capital of Democratic Republic of Congo (DRC). Physicochemical parameters including grain size distribution, organic matter and trace element concentrations were measured in sediment cores sampled from Congo River (n = 3) and Lake Ma Vallée (n = 2). The maximum concentration of trace elements in sediment profiles was found in the samples from the sites of Pool Malebo, with the values of 107.2, 111.7, 88.6, 39.3, 15.4, 6.1 and 4.7 mg kg−1 for Cr, Ni, Zn, Cu, Pb, As and Hg, respectively. This site, which is characterized by intense human activities, is especially well known for the construction of numerous boats that are used for regular navigation on Congo River. Concerning Lake Ma Vallée, the concentration of all metals are generally low, with maximum values of 26.3, 53.6, 16.1, 15.3, 6.5 and 1.8 mg kg−1 for Cr, Ni, Zn, Cu, Pb and As, respectively. However, the comparison of the metal profiles retrieved from the different sampled cores also reveals specific variations. The results of this study point out the sediment pollution by toxic metals in the Congo River Basin. This research presents useful tools for the evaluation of sediment contamination of river–reservoir systems.