Multiple factors affect green roof performance and their effects might vary at different stages of operation. This paper aimed to link green roof performance to hydrologic variables (antecedent moisture condition (AMC) and rainfall intensity) and design variables (growing medium (GM) type and depth) under multiple dimensions at the early stage of operation using laboratory experiment data. The results showed that the AMC is the most influential factor of hydrologic performance, whereas the GM type appeared to primarily affect the nutrient levels of the outflow. The significant main effects of other variables and interaction effects between two variables point to challenges in green roof design.