Green infrastructure (GI) is increasingly being used in urban areas to supplement the function of conventional drainage infrastructure. GI relies on the “natural” hydrological processes of infiltration and evapotranspiration to treat surface runoff close to where it is generated, alleviating loading on the conventional infrastructure systems. This research addresses growing interest in identification and quantification of uncertainties with distributed, infiltration-based stormwater control measures, retrofitted on private and public properties and in right-of-ways in existing urban areas. We identify four major sources of variability and uncertainty in cumulative performance of systems that rely on extensive implementation of distributed GI: non-additive effects of individual best management practices (BMPs) at the catchment scale; the spatial configuration of fine-scale land use and land cover changes; performance changes due to climate change; and noise levels present in urban flow monitoring programs. Using a three-dimensional coupled surface-subsurface hydrological model of a residential sewershed in Washington DC, we find that prolonged, large-magnitude rain events affect various spatial configurations of GI networks differently. Runoff peaks and volumes can both be influenced by the spatial permutations of infiltration opportunities in addition to the absolute magnitude of treated area. However, the magnitude of the last source of uncertainty—noise levels in urban flow monitoring programs—may be larger than sources of variability associated with spatial changes in fine-scale land use and land cover. Changes associated with climate change– more frequent and larger rainfall events– will likely intensify performance differences between spatial configurations of GI but also increase noise levels in urban flow monitoring programs.