Intensive agriculture is an emerging theme of green roof technology, aiming to provide fresh and affordable vegetables for local consumption. The intensification of water and N management is likely to increase the discharge volume and N load to sewers, and atmospheric deposition of heavy metals could compromise food safety. This has not been measured in full-scale rooftop farms and there is little information for land use planning to estimate the environmental and economic returns from rooftop farming. This study is located at the Brooklyn Grange, a 0.6-ha operational rooftop farm atop an 11-story building in New York City. I report the Grange’s balance for water, N, and heavy metals, and address how this balance could be improved in terms of environmental quality, resource use efficiency, and food safety. I found that the discharge volume to sewers was 1.1X the precipitation, and the Grange was a net source for water in the urban watershed. Depending on crop types, water use efficiency was lower than in-ground intensive vegetable production in dry regions, and over half of irrigation was wasted by drainage. Drainage N output was 11 X the atmospheric bulk deposition, and was 5.4X the estimated total atmospheric N deposition, which makes the Grange a net N source in the urban watershed. Fertilizer N input and N leaching loss from soil were similar, and efficiency of N management can be lower than in-ground intensive vegetable production. Efficiency of N and water management could be improved by increasing the soil water storage within the range of plant available water. Atmospheric deposition of Pb and Mn exceeded drainage outputs, and the Grange was a net sink for these metals in the urban environment respectively. There were unwashed vegetable samples exceeding guideline level for Pb, yet the Pb concentration for human consumption was likely to be lower because vegetables are machine-washed before sales. In order to reduce atmospheric deposition of Pb, it is important to cover the soil with mulch.