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Pharmaceuticals, such as non-steroidal anti-inflammatory drugs (NSAIDs) and their metabolites, have become a major concern due to their increasing consumption and their widespread occurrence in the environment. In this paper, we investigate the occurrence of NSAIDs and their metabolites in an urban aquifer, which may serve as a potential resource for drinking water, and propose a methodology to assess the removal of these substances in the river–groundwater interface. Then, risk quotients (RQs) are computed, in order to determine the risk posed by the single NSAIDs and their mixture to human health. To this end, six NSAIDs and two metabolites were collected from an urban aquifer located in the metropolitan area of Barcelona (NE, Spain), in which the major pollution source is a contaminated river. All of the target NSAIDs were detected in groundwater samples, where the concentrations in the aquifer were higher than those found in the river water (except for ibuprofen). Diclofenac, ketoprofen, propyphenazone and salicylic acid were detected at high mean concentrations (ranging from 91.8 ng/L to 225.2 ng/L) in the aquifer. In contrast, phenazone and mefenamic acid were found at low mean concentrations (i.e., lower than 25 ng/L) in the aquifer. According to the proposed approach, the mixing of river water recharge into the aquifer seemed to some extent to promote the removal of the NSAIDs under the sub-oxic to denitrifying conditions found in the groundwater. The NSAIDs that presented higher mean removal values were 4OH diclofenac (0.8), ibuprofen (0.78), salicylic acid (0.35) and diclofenac (0.28), which are likely to be naturally attenuated under the aforementioned redox conditions. Concerning human health risk assessment, the NSAIDs detected in groundwater and their mixture do not pose any risk for all age intervals considered, as the associated RQs were all less than 0.05. Nevertheless, this value must be taken with caution, as many pharmaceuticals might occur simultaneously in the groundwater., IDAEA-CSIC is a Centre of Excellence Severo Ochoa (Spanish Ministry of Science and Innovation, Project CEX2018-000794-S). A. J gratefully acknowledges the support from the Secretary for Universities and Research of the Ministry of Economy and Knowledge of the Government of Catalonia and the Marie Sklodowska-Curie COFUND of the programme H2020 (BP3, contract number 801370). The authors would like to thank the European Commission, the Spanish Foundation for Science & Technology (FECYT) and State Research Agency (AEI)) for funding in the frame of the collaborative international consortium (URBANWAT) financed under the 2018 Joint call of the WaterWorks2017 ERA-NET Cofund. This ERA-NET is an integral part of the activities developed by the Water JPI. Additionally, authors would also thank the Ministry of Science, Innovation and Universities, for funding the projects UNBIASED (Ref: RTI2018-097346-B-I00) under the 2018 call of the “Proyectos de I+D Retos Investigación” and INTEGRATE (Ref: PID2019-107945RJ-I00) under the 2019 call of the “Proyectos de I+D Retos Investigación”.