Green roofs are somewhat deceptive. The plants may be green, but under all that lush growth often lies a dead black petroleum based waterproof membrane. Some green roofs even have multiple layers of perforated polyethylene drainage mats, rigid foam sheets, root-barrier membrane...We didn't go so far, but we did get ourselves a nice fat EPDM sheet.
EPDM pond liners are commonly used as the water proof membrane in green roofs. They're pretty tough, but should be isolated from the roof deck and soil layer, to make sure they don't get punctured. We separated ours with layers of rigid foam insulation. The pond liner wraps up and over the 2x10 fascia to create an enclosed pan for the soil, which drains in the low spots via PVC shower pan drains.
The soil on the roof is the topsoil that used to live where the building is. In creating the pad and footing, we made sure to separate topsoil for the roof, and subsoil for cob. Check back this summer to see how things are growing up there.