The co-occurrence of heavy metals, antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) from hospital effluents spreading into the river receiving systems and evaluating associated risks are topics of scientific interest and still under-studied in developing countries under tropical conditions. To understand the selectors of the ARGs, we examined the occurrence of heavy metals (Cr, Co, Ni, Cu, Cd, Pb and Zn), associated ARB (β-lactam-resistant Escherichia coli , β-lactam-resistant Enterobacteriaceae, and carbapenem-resistant Enterobacteriaceae) and ARGs ( bla _OXA , bla _CTX-M , bla _IMP , bla _TEM ) in water and sediments from two sub-urban rivers receiving urban and hospital effluent waters in the Democratic Republic of the Congo (DRC). High abundances of ARB and ARGs were observed in all sediment samples. All the metal contents correlated negatively with grain size (− 0.94 ≤  r  ≤  − 0.54, p  < 0.05) except for Ni and positively with organic matter content and total copies of 16 s rRNA (0.42 ≤  r  ≤ 0.79, p  < 0.05), except for Ni and Zn. The metals had a significant positive correlation with the faecal indicator Enterococcus except for Ni and Cd (0.43 ≤  r  ≤ 0.67, p  < 0.05). Carbapenem-resistant Enterobacteriaceae correlated negatively with Zn ( r  =  − 0.44, p  < 0.05) and positively with all the rest of toxic metals (0.58 ≤  r  ≤ 1.0, p  < 0.05). These results suggested that some metals had a great influence on the persistence of ARB and ARGs in sediments. Overall, this study strongly recommends the managing urban wastewater to preserve water resources used for human and agricultural purposes. Additionally, we recommend the utilizing biological indicators (faecal indicator bacteria, ARB, ARGs) when investigating urban wastewater pollutions.