The southwest coast of India is exposed to long-period swells propagated from the South Indian Ocean during pre- and post-monsoon seasons. Although swells from the Southern Ocean and Atlantic Ocean were identified in the North Indian Ocean, their existence and impact along the southwest coast of India were not well investigated. On 19 March 2019, the Valiyathura-Shangumukham coastal stretch along the southwest coast of India experienced an unexpected coastal inundation without having a prompt forecast/warning, and not induced by a storm/cyclone in its vicinity. The present study investigates the causative forces of this inundation and estimates the wave runup and inundation. The study reveals that an unusual swell system was developed in the Indian-Atlantic-Southern Oceans (IASO) interface during 10–12 March and propagated towards the southwest coast of India. The measured wave spectra off Varkala clearly depicts the presence of long-period swells (Tp>18 s), which dominantly occurred as single-peaked. Wave modelling has been carried out to characterize the wave transformation associated with the “IASO interface swells” along the southern Kerala coast. A wave runup of up to 0.93 m height and a coastal inundation of up to 83 m onshore have been estimated during this event.