This study assessed the prevalence of fecal indicator bacteria (FIB) and Vibrio species, as well as the physicochemical qualities of the discharged effluents of two wastewater treatment facilities, in the Eastern Cape, South Africa over a one-year sampling period using standard methods. Bacteriological assessment revealed presumptive E. coli counts ranging from 3 to 1.2 × 10 5 CFU/100 mL, while counts of Vibrio spp. ranged from 11 to 1.4 × 10 4 CFU/100 mL. Molecular identification of the isolates by polymerase chain reactions (PCR) yielded positive reaction rates of 76.2% (381/500) and 69.8% (279/400) for E. coli and Vibrio species, respectively. The antibiotic susceptibility profiles of 205 randomly selected PCR-confirmed Vibrio isolates against 18 antibiotics revealed resistance frequencies ranging from 0.5% (imipenem) to 96.1% (penicillin G), based on recommended breakpoint concentrations. About 81% (166/205) of the Vibrio isolates exhibited multidrug resistance (resistance to three or more classes of antibiotics), while nine different antibiotic resistance genes were detected by PCR. The physicochemical qualities of the effluents also ranged as follows: pH (6.5-7.6), temperature (12-27 • C), turbidity (1.5-65.7 mg/L), total dissolved solids (95-171 mg/L), dissolved oxygen (2.1-9.8), electrical conductivity (134-267 µS/cm), free chlorine (0.08-0.72 mg/L), biochemical oxygen demand (0.12-9.81 mg/L), nitrate (1.04-21.5 mg/L), nitrite (0.11-0.76 mg/L), phosphate (1.03-18.3 mg/L) and chemical oxygen demand (27-680 mg/L). The discharged effluents fell short of the regulatory guidelines for some of the parameters assessed. We conclude that the discharged effluents are potential sources of environmental pollution and can contribute to drug resistant bacteria load in the receiving watershed, with the associated ecological and human health risks.