Karst aquifers consist of complex networks of conduits in which groundwater flows and recharge/discharge processes are generally more dynamic than in other types of aquifers. Due to their intrinsic heterogeneity and anisotropy, monitoring, quantifying, and analysing natural responses of karst springs is an efficient tool. Unlike Cenozoic and Mesozoic rocks, in Neoproterozoic karst systems, groundwater circulates and stores generally in dissolution features known as tertiary porosity, as the rock's primary porosity is recrystallized, considered negligible. This article studies the hydrodynamics of a karst portion of the São Miguel River basin, southwest of the state of Minas Gerais, Brazil. The region is predominantly composed of Neoproterozoic carbonate rocks, dating from about 570 to 540 million years ago. During a hydrological year (2019–2020), three karst springs (S1, S2, and S3) were daily monitored through their natural responses (variations of electrical conductivity, EC, temperature, T, and discharge, Q) to rainfall episodes. The data were interpreted based on the analysis of spring hydrographs, time series, recession curves (seasonal and intra‐annual), and statistics of EC, T, and Q variations. The results show the three springs generally exhibit quick flow, typically karstic, in the case of hydrosystems with a well‐structured and functional underground drainage network. The time series indicate the hydrosystem drained by S1 presents slower circulation and a lower degree of linearity, resulting from the higher sinuosity of the system, while the hydrosystems of S2 and S3 have similar behaviours, of quick water circulations immediately after a rainy episode. The degrees of karstification classify S1 and S2 as complex and extensive karst systems consisting of several subsystems, and S3 as a system in which the conduit network is more developed at the upper epiphreatic zone than near the outlet.