The Guarani Aquifer System (GAS) has been studied since the 1970s, a time frame that coincides with the advent of isotopic techniques in Brazil. The GAS isotope data from many studies are organized in different phases: (a) the advent of isotope techniques, (b) consolidation and new applications, (c) isotope assessments and hydrochemistry evolution, and (d) a roadmap to a new conceptual model. The reasons behind the phases, their methodological approaches, and impacts on the regional flow conceptual models are examined. Starting with local δ2H and δ18O assessments of values for water fingerprinting and estimates of recharge palaeoclimate scenarios, studies evolved to more integrated approaches based on multiple tracers. Stable isotope application techniques were consolidated during the 1980s, when new dating approaches dealing with radiogenic and heavy isotopes were introduced. Through the execution of an international transboundary project, the GAS was studied and extensively sampled for isotopes. These results have triggered wider application of isotope techniques, reflecting also world research trends. Presently, hydrochemical evolution models along flow lines from recharge to discharge areas, across large‐scale tectonic features within the entire sedimentary basin, are being combined with residence time estimates at GAS outcrop areas and deep confined units. In a complex system, it is normal that many, and even contradictory hypotheses are proposed, but isotope techniques provide a unique chance to test them. Stable isotope assessments are still needed near recharge areas, and they can be combined with groundwater classical dating procedures, complemented by newer techniques (3H‐3He, CFCs, and SF6). Recent noble gas sampling and world pioneer analytical efforts focused on the confined units in the GAS will certainly led to new findings on the overall GAS circulation. The objective of this article is to discuss how isotope information can contribute to the evolution of conceptual groundwater flow models for regional continental aquifers, such as the GAS.