Population growth has lead to an increase in development and impervious areas in urban settings. Post-development conditions cause several problems for stormwater management such as limited space for stormwater storage systems and the conveyance of pollution picked up by runoff to near by water bodies. Green Roofs with cisterns have been shown to attenuate the peak flow of storm events and reduce the pollution load leaving a site and entering nearby water bodies. The purpose of this research is to expand the available research data on green roofs with cisterns by investigating the water quality and hydrology effects of different green roof designs including depth of media, an additional pollution control layer beneath the growth media, and different drainage layer materials. Furthermore, a comparison study is performed on the cistern water quality, direct filtrate water quality, and control roof filtrate water quality. Results show that phosphorus concentrations are lower when using a pollution control layer beneath the growing media, and that evapotransporation and filtrate factor values from the 4-inch media and the 8-inch media are approximately equal for one year. However, hydrograph results show that the 8-inch media design has a lower peak flow and longer attenuation when compared to the 4-inch media design for a single storm event. Furthermore, the drainage layer material has no significant effect on the water quality or hydrology of the green roof discharge. The data also emphasizes the importance and effectiveness of the incorporation of a cistern into a green roof system.