Few microbial studies in aquaponics, a growing trend in food production, have been conducted to determine food safety status. The aim of this study was to determine the food safety status and the effectiveness of ultraviolet treatment (15 W, luminous flux of 900 lm) as a food safety intervention in reducing the microbial loads of the water system in a model aquaponic unit growing lettuce, basil, and barramundi (Australian Sea Bass). Sweet basil, bibb lettuce, water samples, and fish swabs were collected throughout the 118-day production period, and microbial analysis was conducted in triplicate for the presence of E. coli O157:H7, Salmonella spp., and the prevalence of aerobic plate counts (APC), coliforms, and fecal coliforms in these systems. Absence of foodborne pathogens was confirmed using ELISA technology and enumeration through petrifilms (coliform/E. coli). A significant increase was observed in aerobic plate counts over the trial period (1 to 3 log10 CFU·mL−1) in the presence and absence of UV (p > 0.05). Ultraviolet treatment did not significantly reduce the APC or coliform counts when compared to the control system samples. Future work should focus on improving the unit design, the evaluation of bio-solid filtration, and other food safety interventions.