Since the middle of the 20th century, pollution of freshwater resources by anthropogenic activities constitutes major sources of aquatic environment contamination. In the recent past research is documenting on the prevalence of emerging contaminants in the aquatic ecosystems. In this study we assess the emerging contaminants as well as the prevalence of antibiotic resistant Pseudomonas spp. in the sediments receiving partially/untreated wastewaters and the effects of contamination on the composition and the diversity of bacterial communities in the sediments were explored. Results of the present study highlight the release of emerging contaminants from urban, hospital and WWTP wastewaters. Consequently, sediment receiving systems can act as reservoir for metals, microbes and antibiotic resistance genes which could potentially be transferred to susceptible bacterial pathogens. The remobilization of these contaminants can place the ecosystem and humans at risk. Reduction of contaminants from the sources is recommended for further improvement of water quality.