Anomalous behaviour of specific electrical conductivity (SEC) was observed at a karst spring in Slovenia during 26 high-flow events in an 18-month monitoring period. A conceptual model explaining this anomalous SEC variability is presented and reproduced by numerical modelling, and the practical relevance for source protection zoning is discussed. After storm rainfall, discharge increases rapidly, which is typical for karst springs. SEC displays a first maximum during the rising limb of the spring hydrograph, followed by a minimum indicating the arrival of freshly infiltrated water, often confirmed by increased levels of total organic carbon (TOC). The anomalous behaviour starts after this SEC minimum, when SEC rises again and remains elevated during the entire high-flow period, typically 20–40 µS/cm above the baseflow value. This is explained by variable catchment boundaries: When the water level in the aquifer rises, the catchment expands, incorporating zones of groundwater with higher SEC, caused by higher unsaturated zone thickness and subtle lithologic changes. This conceptual model has been checked by numerical investigations. A generalized finite-difference model including high-conductivity cells representing the conduit network (“discrete-continuum approach”) was set up to simulate the observed behaviour of the karst system. The model reproduces the shifting groundwater divide and the nearly simultaneous increase of discharge and SEC during high-flow periods. The observed behaviour is relevant for groundwater source protection zoning, which requires reliable delineation of catchment areas. Anomalous behaviour of SEC can point to variable catchment boundaries that can be checked by tracer tests during different hydrologic conditions.