This study proposes an analysis methodology to address how very rare marine extremes can be understood using limited data. In summer 2016, extreme weather and marine events occurred simultaneously around the Pacific shelf off southeastern Hokkaido, Japan. Six successive tropical storms brought extreme precipitation and an anticyclonic mesoscale eddy of subtropical Kuroshio water closely approached the coast, locally causing marine heat waves. We examined how these compound extremes affected oceanographic conditions on the coastal shelf by analyzing data from ship surveys in October 2016 on the Pacific shelf and outputs from a realistic ocean model. Climatologically, warm, high-salinity (33.0–33.7) subtropical water from the Okhotsk Sea (modified Soya Warm Current water) is distributed near the sea surface on the Pacific shelf in October and transported by the along-shelf boundary current. In 2016, however, a vertically well-mixed low-salinity (<33.0) layer associated with the heavy rainfall was observed at 0–50 m depth on the shelf, salinity maxima (≥33.7) associated with Kuroshio water from the mesoscale eddy occurred at 50–150 m depth on the slope, and baroclinic jets formed along the salinity front near the shelfbreak. These observed salinity structures were reproduced by a 1/50° ocean model. Particle-tracking experiments revealed that the low-salinity water originated mainly off eastern Hokkaido, where heavy rainfall events occurred in August, and was modified by mixing with Soya Warm Current water before transport to the Pacific shelf.