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Coastal aquifers are complex systems governed by fresh–saline water interactions and ocean tidal effects. The vertical electrical conductivity (EC) and temperature (T) are general indicators for detecting the fresh–saline water interface (FSI) and sea water intrusion in groundwater wells located in coastal aquifers. In this method brief, we developed a cost‐effective Arduino‐based automatic‐vertical profile monitoring system (A‐VPMS) to continuously record vertical EC and T in groundwater wells, with the aim of testing its effectiveness in spatiotemporal monitoring of the FSI in a coastal aquifer located in eastern Korea. By analyzing the high‐density EC and T data obtained by the A‐VPMS, we evaluated the characteristics of the FSI, such as depth and spatial distribution. Our established EC and T data collection method using the A‐VPMS proved to be efficient and reliable, providing an excellent tool for fine‐scale temporal and spatial understanding of sea water intrusion. The results of this study demonstrate the potential of the A‐VPMS for continuous monitoring of the FSI in coastal aquifers, which is crucial for sustainable management of groundwater resources. Article impact statement: New automatic monitoring system captures high‐density coastal aquifer data, providing insights into fresh‐saline water interface dynamics. [ABSTRACT FROM AUTHOR]