•Hydrogeological, chemical, and isotopic data assess antibiotic pollution in groundwater.•Most frequent antibiotics are sulfamethoxazole and ciprofloxacin.•A lack of spatial correlation exists for antibiotic occurrence, yet not for nitrate.•Fate of antibiotics in groundwater not only depend on chemical properties but on hydrogeology. Display omitted Antibiotics are an increasing focus of interest due to their high detection frequency in the environment. However, their presence in water bodies is not regulated by environmental policies. This field study investigates, for the first time, the occurrence, behavior and fate of a selection of 53 antibiotics, including up to 10 chemical groups, in an alluvial aquifer originated from manure application in an agricultural region using hydrogeological, hydrochemical and isotopic approaches. Up to 11 antibiotics were found in groundwater corresponding to 4 different chemical groups: fluoroquinolones, macrolides, quinolones and sulfonamides. In surface water, only 5 different antibiotics from 2 chemical groups: fluoroquinolones and sulfonamides, were quantified. The most frequent antibiotics were sulfamethoxazole and ciprofloxacin. Concentrations of antibiotics were in the order of ng/L, with maximum concentrations of 300ng/L in groundwater. Hydrochemistry and isotopic data and geostatistics confirmed the spatial trend observed for nitrates, where nitrate concentrations tend to be higher in the margin areas of the study area, and lower concentrations are found nearby the river. On the other hand, no clear continuous spatial concentration trend of antibiotics was observed in the aquifer, supported by the short spatial correlation found in the variograms. This indicates that the physical-chemical properties and processes of each antibiotic (mainly, sorption and degradation), and other environmental issues, such as a patchy diffuse input and the manure antibiotic content itself, play an important role in their spatial distribution in groundwater. A discussion on the estimation of the antibiotic sorption parameter reveals the difficulties of describing such phenomena. Furthermore, retardation factors will extend over several orders of magnitude, which highly affects the movement of individual antibiotics within the aquifer. To summarize, this study points out the difficulties associated with antibiotic research in groundwater in order to define water resources quality management strategies and environmental regulations.