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In the current context of population growth and climate change, it is essential to effectively manage groundwater resources, to improve their quality, and to determine the behaviour of certain contaminants. Groundwater quality can be worsened most often by anthropogenic factors but can also be altered by natural factors depending on the chemical signatures of water sources (i.e., hydrochemical reactions) as a result of mixing processes. In these cases, the use of mixing calculations and multivariate statistical analysis (MSA) methods is crucial for determining the reactions that occur, the origin and fate of the detected compounds, ions or parameters, and the behaviour of the system. Thus, these methods ascertain processes that affect the chemical composition (i.e., quality) of groundwater bodies, and this information is needed for designing groundwater management strategies that exploit aquifers in a sustainable way. However, these methods are rarely employed, as few investigations that consider them focus on urban aquifers. Here, mixing calculations and other MSA methods that consider major ions and environmental isotopes are utilized in an aquifer located in a rural area associated with the Niebla-Posadas aquifer, Spain, where groundwater quality has deteriorated due to geogenic factors. This study proves the usefulness of these methods for deriving essential information that is needed (1) to properly manage the exploitation of aquifers, (2) to avoid the deterioration of groundwater bodies, and (3) to identify the reasons behind poor groundwater quality., Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. This study was supported by the “Agencia Estatal de Investigación” from the Spanish Ministry of Science and Innovation and the IDAEA-CSIC, a Centre of Excellence Severo Ochoa (CEX2018-000794-S). EP gratefully acknowledges the support received through the grant RYC2020-029225-I funded by MCIN/AEI/ 10.13039/501100011033 and by “ESF Investing in your future” and the Award for Scientific Research into Urban Challenges in the City of Barcelona 2020 (20S08708) from the Barcelona city council. RC gratefully acknowledges the financial support from the Balearic Island Government through the Margalida Comas postdoctoral fellowship programme (PD/036/2020). The authors would like to thank the European Commission, the Spanish Foundation for Science and Technology (FECYT) and Spanish 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, the authors would also like to thank the Ministry of Science, Innovation and Universities, for funding the project UNBIASED (Ref: RTI2018-097346-B-I00) under the 2018 call of the “Proyectos de I+D Retos Investigación.