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Abstract The global increase of urban impervious land cover poses a significant threat to the integrity of river ecosystems. Hence, it is critical to assess the efficiency of green roofs (GR) to mitigate the negative impacts of urbanization on river ecosystems, such as thermal surges and pollutants. In this study, we evaluated the ecohydrological behaviour of two fully established GR under differing management regimes at the Chicago Botanical Gardens from July to September 2019. The drainage outflow from a non‐vegetated roof, a managed GR (perennial native and non‐native plants) and an unmanaged GR (perennial natural prairie vegetation) were monitored, and thermal dynamics, dissolved organic matter (DOM) composition and nitrate concentration assessed. The managed GR runoff had a lower DOC concentration and less humic‐like DOM signal (SUVA₂₅₄) compared to the unmanaged GR. In contrast, lower concentrations of nitrate and more recalcitrant DOM (less protein‐like compounds relative to humic‐like compounds) were associated with the unmanaged GR. The unmanaged GR also displayed a greater capacity to reduce thermal surges associated with storm events. Our study provides new information on the implications of GR management for water quality with particular relevance to the urban stream syndrome. Further, the impacts of GR management on the mitigation of thermal surges and DOM composition can help to improve future GR design, as these ecohydrological responses have been largely overlooked to date. Our findings can support future urban planning, particularly for scenarios where green infrastructures are used to mitigate the impacts of climate change on urban river ecosystems.