Groundwater is essential in the management of water resources globally. The water quality of aquifers is affected by climate change and population growth, aspects that can be addressed with stable isotope analysis. This study aims to carry out an analysis of the scientific information related to groundwater and stable isotopes (GSI) using scientific databases (Scopus and Web of Science) to evaluate the intellectual structure of the subject and the emerging research lines. The methodology includes: (i) topic search selection, (ii) tools in databases processing, (iii) bibliometric analysis, and (iv) review by clustering technique. The results showed that the scientific production of GSI can be addressed through three evolution periods: I (1969–1990), II (1991–2005), and III (2006–2021). Periods I and II did not significantly contribute to publications because, in the past, most of the student’s thesis (M.Sc. and Ph.D) consisted of writing a report that summarizes their works. Therefore, the researcher was not obliged to publish their results in a professional journal. Finally, the third period showed exponential growth, representing 82.34% of the total publications in this theme because, in the last years, institutions require at least one scientific article depending on the country and university, in order to graduate with an M.Sc. and PhD. Finally, the contribution of this study is reflected in the recognition of new research lines and their applicability by the knowledge of recharge sources, environmental aspects, infiltration, knowledge of the aquifer-meteoric water system, and groundwater-superficial water interaction. These aspects offer the possibility of analyzing integrated water resources management at the watershed or river-aquifer systems level.