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River and stream ecosystems within cities can provide important Ecosystem Services (ES) to urban population along with the maintenance of biodiversity. Increasing urbanization with land use change can affect biodiversity, impacting ES provision, but the relationships between biota and ES are complex and poorly understood. This study aims to explore relationships between aquatic biodiversity (communities’ composition and structure), urbanization and ES provided by urban streams. Nine streams were surveyed within a city area (up to 8 km of the city centre) focusing on common biological indicators (i.e., macroinvertebrates and diatoms), as well as several indicators of Provisioning (N = 7), Regulation (N = 14) and Cultural (N = 23) services for this type of ecosystem. Urban stream sampling sites were also assessed in terms of their urbanization degree, according to the surrounding imperviousness area (IMD). Pearson correlations showed trends of negative relationships between IMD and both Provisioning and Regulating services. Yet, urbanization effects on the biota seemed to be mitigated due to enhanced hidromorphological site features. The community structure and composition of invertebrates and diatoms was differently associated to ES (BIOENV analysis). Whereas macroinvertebrate communities related specifically with Provisioning and Regulating indicators, the diatom responded just to regulating indicators. Overall, this study showed that aquatic biodiversity is linkable with ES provided by urban streams, and such relationship depends on specific ES indicators mainly for Provisioning and Regulating services. Additionally, macroinvertebrate communities can be used as a suitable indicator for the potential of streams in supplying Provisioning and Regulating ecosystem services. This shows that their indicator value goes beyond their known potential as indicators of structural and functional integrity of river ecosystems. These results also reinforce the need to protect nature associated to running water ecosystems in urbanized areas, as they provide green and blue solutions for the sustainability of cities.