Analysis of water table fluctuations can provide important insight into the hydraulic properties and structure of a coastal aquifer system including the connectivity between the aquifer and ocean. This study presents an improved approach for characterizing a permeable heterogeneous coastal aquifer system through analysis of the propagation of the tidal signal, as well as offshore storm pulse signals through a coastal aquifer. Offshore storms produce high wave activity, but are not necessarily linked to significant onshore precipitation. In this study, we focused on offshore storm events during which no onshore precipitation occurred. Extensive groundwater level data collected on a sand barrier island (Sable Island, NS, Canada) show nonuniform discontinuous propagation of the tide and offshore storm pulse signals through the aquifer with isolated inland areas showing enhanced response to both oceanic forcing signals. Propagation analysis suggests that isolated inland water table fluctuations may be caused by localized leakage from a confined aquifer that is connected to the ocean offshore but within the wave setup zone. Two‐dimensional groundwater flow simulations were conducted to test the leaky confined‐unconfined aquifer conceptualization and to identify the effect of key parameters on tidal signal propagation in leaky confined‐unconfined coastal aquifers. This study illustrates that analysis of offshore storm signal propagation, in addition to tidal signal propagation, provides a valuable and low resource approach for large‐scale characterization of permeable heterogeneous coastal aquifers. Such an approach is needed for the effective management of coastal environments where water resources are threatened by human activities and the changing climate.