There are increasing concerns about wastewater treatment plants (WWTPs) acting as hotspots for antibiotic resistance genes (ARG). However, their role largely depends upon the treatment methods and antibiotics in the wastewater. To better understand these influences, we compared the occurrence and fate of ARG between a pond system in a developing country (Namibia) and an advanced WWTP (activated sludge system) in a developed country (Germany). A targeted metagenomic approach was used to investigate the wide-spectrum profiles of ARGs and their co-occurrence patterns at both locations. In total, 93 ARG subtypes were found in the German influent wastewater, 277 in the Namibian influent wastewater. The abundant ARG types found in Namibia and Germany differed, especially for multidrug resistance genes. The differences in occurrence and reduction can help to understand the performance of simple WWTP such as pond systems common in Namibia, where direct contact with wastewater is a potential risk for contamination.