Antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) are globally considered emerging environmental contaminants that pose a serious concern to human health and the ecosystem. The objective of the study was to detect the abundance of bacteria, characterize their antibiotic resistance phenotypic and genotypic characteristics in Palapye wastewater treatment facility (PWWTF), Gaborone wastewater treatment plant (GWWTP) and the downstream environments. The two chosen study areas are different in terms of population, wastewater treatment infrastructures and uses of final effluent. Culture dependent and independent approaches were used to determine occurrence, diversity and abundance of potentially pathogenic and antibiotic resistant bacteria and ARGs in wastewater influent, effluent and downstream environments samples. In PWWTF, 39% antibiotic resistant bacteria were detected in the influent, 25% in the effluent and 35% were detected in downstream environment. In GWWTP, the bacteria isolated with resistance to antibiotics were 36% in the influent, 39% in the effluent wastewater and the downstream environment had 25%. The ARB bacterial species detected were; Staphylococcus species, E.coli, presumptive E.aerogenes, Pseudomonas species, Brucella species, Salmonella species, Listeria species and Campylobacter species. The study also detected ARGs; tetA (tetracycline), mphA (macrolide), strB (streptomycin), sul1 (sulphonamide), dfr (trimethoprim) and int1 (mobile ARG cassette) in all the sample sources including the downstream environments. The results reveal occurrence and diversity of clinically relevant ARB and ARGs that accumulate in wastewater treatment facilities and subsequently disseminated to the downstream environments, particularly water sources. This research is critical in the development of new water quality monitoring schemes and implementation of policies on the use of effluent water for irrigation purposes.