Karst aquifers contribute to supplying drinking water to almost a quarter of the world´s population. Their complex dynamics requires specific approaches aimed at recognizing their singularities, analyzing its vulnerability, and ensuring water resources quality. In this paper, the results of processing and modeling five breakthrough tracer curves obtained under different hydrodynamic conditions in the main conduit of Egino karst aquifer (Basque Country, Spain) are analyzed together with those involving pressure injections of the tracer in the saturated zone of the karst massif recharge area. In the conduit, transport is immediate and highly efficient (recovery rates above 84% and dispersion coefficients from 15.04 to 84.35 m 2 /min); tracer retentions increase as flow rates decrease and no significant contributions to its surroundings are observed. In contrast, tracer transport from the massif recharge area is more complex: after injection at a pressure of 1 MPa, most tracer remains in the surrounding of the injection borehole, retained in a saturated medium of low effective fracture porosity ( ϕ f  = 1.02 × 10 −4 , assuming a radial divergent flow model); subsequently, the main tracer mobilization to the spring was registered with the first rains, with 0.088 m/min mean velocity and high concentrations per unit mass being injected ( C p / M 0  = 0.03 mg/L/kg), which is evidence that the tracer reaches soon the karst conduit network. In any case, a decreasing tracer presence is registered at the injection zone during a hydrological cycle. In both cases, the observed non-linearity of transport processes should be considered in the development of vulnerability approaches, modeling efforts, and mapping. Furthermore, in the case of karst massif recharge areas, as the presence of pollutants may have a significant impact on the springs and persist over time, their management and protection needs must be revised in each specific site. Simultaneously, quality-monitoring programs at the springs must be adapted to the aquifers recognized dynamics.