Sediments from two rivers receiving animal farming wastewaters under tropical conditions in Kinshasa, capital city of the Democratic Republic of the Congo were investigated for microbial pollution. The total bacterial load, the abundance of relevant bacteria and ARGs via qPCR. The total bacterial load correlated with relevant bacteria and genes blaOXA-48, sul3, and tet(B) (P value<0.01). E. coli strongly correlated with 16S rDNA, Enterococcus, Pseudomonas spp., blaOXA-48, sul3, and tet(B) (P value<0.01) and with blaCTX-M, sul1, and sul2 at a lower magnitude (P value <0.05). The most abundant and most commonly detected ARGs were sul1, and sul2. In a similar manner, we investigated hospitals and toxic metals and persistent organic pollutants and their consequences on sustainable agriculture and the risk posed to the consumers.