Submarine springs that drain inland karst aquifers may be subject to abrupt flow reversals in which alternatively freshwater outflows to the sea or saltwater inflows into the aquifer. Here we provide a full flow reversal long-duration data time series at the Vise spring (below Thau lagoon, south of France) during which saltwater inflows into the aquifer. We demonstrate that the driving parameter of the hydrosystem regime shifts is the hydraulic gradient between the aquifer and the lagoon, controlled by water density changes. We reveal the existence of two tipping points: (i) below a hydraulic gradient threshold, the hydrosystem suddenly degrades from a normal regime to saltwater intrusion, and (ii) a much larger hydraulic gradient is necessary for the recovery of the hydrosystem. The high hysteresis of the hydrosystem, due to the vertical karst conduit filling by saltwater, is responsible for the long duration of the degradation and saltwater intrusion. In a changing climate context, flow reversal at submarine karst springs could be more frequent and longer in the future due to sea level rise and a decrease in recharge, threatening inland or offshore freshwater resources.