Monitoring of self‐potentials (SP) in the Chalk of England has shown that a consistent electrical potential gradient exists within a coastal groundwater borehole previously affected by seawater intrusion (SI) and that this gradient is absent in boreholes further inland. Furthermore, a small but characteristic reduction in this gradient was observed several days prior to SI occurring. We present results from a combined hydrodynamic and electrodynamic model, which matches the observed phenomena for the first time and sheds light on the source mechanisms for the spatial and temporal distribution of SP. The model predictions are highly sensitive to the relative contribution of electrochemical exclusion and diffusion potentials, the ‘exclusion efficiency’, in different rock strata. Geoelectric heterogeneity, largely due to marls and hardgrounds with a relatively high exclusion efficiency, was the key factor in controlling the magnitude of the modelled SP gradient ahead of the saline front and its evolution prior to breakthrough. The model results suggest that, where sufficient geoelectric heterogeneity exists, borehole SP may be used as an early warning mechanism for SI.