Urban rooftop agriculture is a growing enterprise in the US with the goal of providing high quality, healthy, locally grown produce for city dwellers. However, air pollution abatement and the purification of stormwater are among the ecosystem services emphasized in studies of conventional green roofs. If rooftop farms actually capture pollutants, then accumulation of heavy metals in the soil could pose a problem over time. This study reports the heavy metal concentrations in soil, atmospheric deposition, and drainage output of 8 metals from the Brooklyn Grange Navy Yard Farm, rooftop vegetable farm in New York City, USA. Drainage of Pb and Mn were 6% and 14% of atmospheric bulk deposition, respectively, meaning that the Grange could be a net sink for Pb and Mn. Although there were small scale hotspots in the soil, farm-wide averages for heavy metal concentrations never exceeded guideline levels, and relatively low concentrations of Pb and Ba in the soil suggest that rooftop soils may be less vulnerable to contamination related to traffic and construction. In comparison to the growing seasons, we found relatively high concentrations of Pb and Cr in the soil during fallow periods when the soil was bare. To reduce the atmospheric deposition of heavy metals to soil, it is important to cover the soil with mulch, and discard the used mulch and unmarketable portion of vegetables, instead of recycling them via composting for soil amendments.