Many atolls in tropical oceans are under the threat of sea‐level rise. Mitigation planning requires reliable estimates of increasing wave runup in response to sea‐level rise and changes in wave climate. However, shoreline dynamics on reef‐lined coasts, particularly the effect of low‐frequency waves, are not yet fully understood. Herein, we present a field study on the southernmost atoll of the Maldives to clarify the variability of shoreline water levels driven by waves and tides. The atoll is located just south of the equator and has a moderate wave climate; it is occasionally impacted by long‐distance swells from the South Indian Ocean. Wave evolution on a reef‐lined coast was observed in situ for a period of seven months. The shallow water depth tightly constrains reef‐flat waves under normal wave conditions; however, this constraint is broken under extreme conditions by low‐frequency waves generated from long‐period swells. Particularly, very low‐frequency waves (<0.005 Hz) are amplified via wave resonance over the reef platform and significantly contribute to shoreline motions. Our observation of shoreline motions confirmed that, under energetic conditions, extreme wave run‐ups are characterized by swell run‐ups riding on crests of low‐frequency waves. A combined approach of observations and analytical modeling revealed the long‐term variability of shoreline water levels, highlighting the stochastic nature of extreme water levels influenced by a joint probability of far‐field swells and high tides. Our results suggested that extreme shoreline water levels would increase at a significantly higher rate than sea‐level rise in the future. An atoll is a ring‐shaped coral reef on which a series of islands (having ground elevations of less than a few meters) have formed. Inhabited atolls in tropical oceans are, therefore, considered to be one of the most vulnerable areas to global sea‐level rise, because this rise will exacerbate wave‐induced flooding in island communities. Adaptation strategies require reliable estimates of increasing wave impacts; however, it is often difficult to assess shoreline water levels driven by waves and tides over actual reef topography of diverse forms. This study investigated wave processes on the southernmost atoll of the Maldives, where there is a strong influence from waves traveling from the South Indian Ocean. Our wave observations revealed that extreme shoreline water levels were driven by short waves riding on crests of relatively long waves that developed over the reef platform. The long‐period waves are generated from a group of high swells over the outer reef platform and are significantly amplified when their period coincides with the natural period of the reef water. The study clarified the shoreline dynamics on the reef‐lined coast and demonstrated that extreme shoreline water levels would increase at a higher rate than sea‐level rise in the future. A combination of observations and analytical modeling clarified the variability of shoreline water levels on the atoll of the MaldivesWave runup under energetic conditions is characterized by swell runup modulated by dominant very low‐frequency waves (<0.005 Hz)Extreme shoreline water levels on the reef‐lined coast occur with a joint probability of far‐field energetic swells and high tides A combination of observations and analytical modeling clarified the variability of shoreline water levels on the atoll of the Maldives Wave runup under energetic conditions is characterized by swell runup modulated by dominant very low‐frequency waves (<0.005 Hz) Extreme shoreline water levels on the reef‐lined coast occur with a joint probability of far‐field energetic swells and high tides