Climate change is stressing irrigation water sources, necessitating the evaluation of alternative waters such as harvested rainwater to determine if they meet water quality and food safety standards. We collected water, soil, and produce samples between June and August 2019 from two vegetable rain garden (VRG) sites in Frederick, Maryland that harvest rainwater using a first flush system, and deliver this water to produce through subsurface irrigation. The raised VRG beds include layers of gravel, sand, and soil that act as filters. We recorded the average surface soil moisture in each bed as well as antecedent precipitation. All water (n = 29), soil (n = 55), and produce (n = 57) samples were tested for generic E. coli using standard membrane filtration, and water samples were also tested for Salmonella spp. and Listeria monocytogenes by selective enrichment. No Salmonella spp. or L. monocytogenes isolates were detected in any water samples throughout the study period. Average E. coli levels from all harvested rainwater samples at both sites (1.2 and 24.4 CFU/100 mL) were well below the Good Agricultural Practices food safety guidelines. Only 7 % (3/44) of produce samples from beds irrigated with harvested rainwater were positive for E. coli. E. coli levels in soil samples were positively associated with average surface soil moisture (r = 0.13, p = 0.007). Additionally, E. coli presence in water samples was marginally associated with a shorter length of antecedent dry period (fewer days since preceding rainfall) (p = 0.058). Our results suggest that harvested rainwater collected through a first flush system and applied to produce through subsurface irrigation meets current food safety standards. Soil moisture monitoring could further reduce E. coli contamination risks from harvested rainwater-irrigated produce. First flush and subsurface irrigation systems could help mitigate climate change-related water challenges while protecting food safety and security.