The Lagoa Santa Karst Environmental Protection Area is known worldwide as the place where the oldest human fossil in the Americas was found. Beyond its archaeological richness is speleological, faunistic and floristic richness across this remarkable karstic landscape. It is also a region with important aquifers for public and private water supply. Located in the state of Minas Gerais, Brazil, despite its environmental relevance, the area is characterized by increased anthropic environmental impacts. Regarding the relationship between surface water and groundwater, in order to investigate the annual input of water into the aquifers, this study aimed to estimate the annual recharge rate in the hydrological years 2017 to 2021 using three methods: the recession curve displacement method of Rorabaugh (International Association of Scientific Hydrology, 1964, 63:432–441), the recursive digital filter method by Lyne and Hollick (Institute of Engineers Australia National Conference, 1979, pp. 89–93), and the method based on water‐table fluctuation in tubular wells proposed by Healy and Cook (Hydrogeology Journal, 2002, 10(1):91–109). The average percentage of rainfall that is recharged into the aquifer, considering the overall period studied from 2017 to 2021, found with the three methods was 13%, 9% and 9%, respectively, which indicates that recharge rates within the study area are low and that higher values are observed within karst basins in comparison with basins located in pelitic zones. Overall, the methods yielded coherent values among each other and were compared with previous studies in the area. In relation to the automatized recursive digital filter method, the automatized recession curve displacement method was more adherent because it considers daily streamflow measurements. The WTF method was handy for the local recharge rate analysis and enabled an evaluation of recharge rates in each aquifer unit. Despite the similarity of the values obtained in the methods, they are likely underestimated due to the high pumping rates of groundwater. Furthermore, it is recommended to deepen the correlation between lithotype, karst geomorphology, and its dissolution processes to improve the understanding of recharge processes.