There is a lack of understanding of how urban aquatic nature-based solutions (aquaNBSs) affect ecohydrology and how they in turn are affected by urbanization and climate change. We use a multi-tracer approach of stable water isotopes, hydrochemistry, and microbial and macrophyte diversity to disentangle the effects of hydroclimate and urbanization. The results show potential limitations of aquaNBSs regarding water quality and biodiversity in response to hydroclimate and urban water sources.