The occurrence and dissemination of toxic metals, antibiotic resistant bacteria and their resistance genes (ARGs) in the aquatic ecosystems of sub-Saharan African countries are still understudied, despite their potential to threat human health and aquatic organisms. In this context, the co-contamination and seasonal distribution of toxic metals and ARG in river sediments receiving untreated urban sewages and hospital effluents from Kinshasa, the capital city of the Democratic Republic of the Congo were investigated. ARGs including β-lactam resistance (blaCTX-M and blaSHV), carbapenem resistance (blaVIM, blaIMP, blaKPC, blaOXA-48 and blaNDM) and total bacterial load were quantified by using quantitative polymerase chain reaction (qPCR) in total DNA extracted from sediment. The amount of toxic metals in sediments was quantified using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). The results highlight high abundance of 16S rRNA and ARGs copy numbers in sediment samples. Strong pollution of rivers by toxic metals was found, with max values (mg kg−1) of 81.85(Cr), 5.09(Co), 33.84 (Ni), 203.46 (Cu), 1055.92(Zn), 324.24(Pb) and 2.96(Hg). Results also highlight the high abundance of bacterial markers (8.06 × 109-2.42 × 1012 16S rRNA g−1 DS) as well as antibiotic resistance genes (up to 4.58 × 108 ARG g−1 DS) in the studied rivers. Significant correlations were observed between (i) metals (except Cd and Hg) and organic matter (R>0.6, p<0.05); and (ii) ARGs (except blaNDM) and 16S rRNA (R>0.57, p<0.05). Results demonstrated that multi-diffuse pollution originating from human activity contribute to the spread of toxic metals and ARGs into the aquatic ecosystems.