This research presents a case study that examines an upper-ocean salinity response to intense rainfall using 4 years of observed salinity data from the Aquarius and Argo floats. The Aquarius sea surface salinity (SSS) in the subtropical region of the North Pacific reveals a notable event in which SSS is locally freshened by intense rainfall. Although the SSS pattern shortly after the rainfall reflects the atmospheric pattern, its final form reflects the ocean’s dynamic structure; low-salinity water distributes in the shape of an anticyclonic eddy. Observations using Argo profiling floats confirm that low-salinity water dominates the entire water column of the eddy above 70 m. We found that an eddy stirring effect would play an important role in forming the eddy-shaped low-salinity water. As a precondition, intense rainfall on the tropical side enhances the meridional gradient of background SSS with freshened low-salinity water to the south and saline water to the north. The anticyclonic eddy located at the enhanced SSS front stirs the water in a clockwise direction. Specifically, northward flow in the western side of the eddy transports fresh water, whereas southward flow in the eastern side transports saline water. As this northward–southward flow moves the eddy to the west where the transported fresh water is dominant as a baroclinic Rossby wave, this dynamic process would form the eddy-shaped low-salinity water. This clear view of such eddy stirring is due to the inherent nature of the subtropical region that is characterized by less frequent precipitation.