Water supply from karst sources is a worldwide natural resource and the exploitation is tied to the knowledge of the positions of the hydrologic channels. We show that surface deformation induced by flood events in karst conduits is observable, and consists in uplift and outward movement from the hydraulic channel. Precipitation events produce the natural occurrence of subsurface hydraulic overpressure up to 1 MPa. Numerical modeling shows that the stresses are so strong to uplift and dislocate the surface by several mm and induce tilts in the order of microradians. The naturally induced deformation is compatible with a transient internal pressure loading of a channel. The results can be used to find new channels with dense GNSS networks. Sea water incursion and channels accessed for tourism could be monitored. Seismicity has been shown to have a seasonal variation in some areas, which could be explained by the subsurface stresses induced by the natural subsurface overpressure. The pressure induced deformation is expected to be observed in all karstic systems worldwide.