The appearance and spread of antibiotic resistance are considered a highly complex process with many factors affecting the resistance mechanisms, including metals. In order to fully understand the spread of antibiotic resistance in different environments, combined studies including geochemistry and microbiology are becoming imperative. So far, very few such studies have been conducted, and none of them involves the southernmost regions. The aim of this study was, therefore, to examine the biogeochemical characteristics of sediments of the southernmost part of Chile. Sediment geochemistry, as well as the presence of heterotrophic and carbapenem-resistant bacteria (CRB) in the Río de las Minas and neighbouring Strait of Magellan in Punta Arenas (Chile), was investigated to assess the anthropogenic impact of untreated urban wastewater on the accumulation of metals and microbial contaminants in this coastal system. Geochemistry of sediments indicated the influence of both natural processes and anthropogenic activities. Although levels of metals in sediments currently do not represent a toxic effect on organisms, the anthropogenic influence on the sediment composition in the study area cannot be denied. Clinically relevant CRB were found in river sediments (1.9 and 2.7 log CFU / mL). Our findings suggest that the Río de las Minas is under the anthropogenic impact of untreated urban wastewater and represent a significant source of potentially pathogenic CRB to the local environment.