Lotic and lentic urban waters – through interactions and interlinked functions – can provide multiple ecosystem services if properly managed. However, as the objectives of urban watershed management have grown over time from a singular focus on flood mitigation to a diverse range of goals (e.g., water quality, recreation, flow regime, biodiversity), so have the challenges associated with achieving multiple endpoints in complex networks. Due to space, design, funding, or ecological limitations it is questionable if certain co-benefits can be compatible within the same space. For example, a system designed to retain pollutants may cause disservices that directly impact wildlife (e.g., metal toxicity, disease or parasite burden); the installation of poorly-designed inline treatment wetlands may impact biota adapted to lotic systems; and systems designed with the intent to capture greenhouse gases (likely with large amounts of vegetation) may be less useful for fishing or boating. While networks of constructed and remnant natural waters may be viewed as novel ecosystems with no historic point of comparison, through a different lens they might be a return to historical morphology and function. This too raises important questions about how or if those historical baselines can be identified and whether they should always be the goal. Targeted studies can address these challenges. The SUSE workshop introduced here will lay out a research agenda to understand ecosystem service tradeoffs in urban waters, with the intent to maximize net benefits.