A model is developed to account for antibiotic resistance genes (ARGs) as both intracellular DNA (iDNA) and extracellular DNA (eDNA) in predicting the fate and transport of ARGs in receiving waters downstream of wastewater treatment plants (WWTPs). eDNA can contribute to iDNA concentrations of ARGs through horizontal gene transfer (i.e., transformation); however, the prevalence of eDNA and its effects have not been addressed in previous field studies and predictive models. The present model tracks eDNA and iDNA in both the water column and the sediment, and it includes physical, chemical, and biological processes. It also provides a framework for systematically identifying conditions under which accounting for eDNA is important. For example, when the timescale for transformation is small compared with the timescale for advection and the water column concentration of eDNA is large compared with that of iDNA, ignoring eDNA can underpredict the total amount of ARGs significantly (e.g., by an order of magnitude or more). The model demonstrates that the eDNA fraction of ARGs in WWTP discharges is important to include in predictions for improved risk assessment of antibiotic resistance in the aquatic environment.