Managed Aquifer Recharge is an increasingly prevalent solution to sustain water availability in arid regions. Recharge of groundwater resources using treated wastewater effluent is one type of managed aquifer recharge that offers long-term sustainable water management. However, there are some concerns regarding the reuse of wastewater and its potential to increase exposures to antibiotic resistant bacteria and antibiotic resistance genes that could affect human health. Antibiotic resistance genes can confer the ability for bacteria to resist antibacterial treatment, rendering their presence in water supplies as an area of research needed to evaluate where environmental “hot spots” of potential antibiotic resistance disseminate. To evaluate the occurrence of antibiotic resistant bacteria and antibiotic resistance genes, sampling of an Arizona managed aquifer recharge facility was performed, with target antibiotic resistance genes measured using quantitative polymerase chain reaction. The occurrence of antibiotic resistance genes was evaluated at several sampling wells and in sediments to examine trade-offs between water quantity benefits and water quality issues. The goal of this work is to inform management operations for secure water quality in the face of climate change.