Since 2007, the University of Genoa has been carrying out a monitoring programme to investigate the hydrologic response of green roofs in the Mediterranean climate by installing a green roof experimental site. In order to assess the influence of green roofs on the storm water runoff quality, water chemistry data have been included in the monitoring programme since 2010, providing rainfall and outflow data. For atmospheric source, the bulk deposition is collected to evaluate the role of the overall atmospheric deposition in storm water runoff quality. For subsurface outflow, a maximum of 24 composite samples are taken on an event basis, thus aiming at a full characterization of the outflow hydrograph. Water chemistry data reveal that the pollutant loads associated with green roof outflow is low; in particular, solids and metal concentrations are lower than values generally observed in storm water runoff from traditional rooftops. The concentration values of chemical oxygen demand, total dissolved solids, Fe, Ca and K measured in the subsurface outflow are significantly higher than those observed in the bulk deposition (p < 0.05). With respect to the atmospheric deposition, the green roof behaviour as a sink/source of pollutants is investigated based on both concentration and mass.