Nagahama Bay of Satsuma Iwo-Jima Island, southwest Japan, is an excellent place for studying sedimentation of iron-oxyhydroxides by shallow-marine low-temperature hydrothermal activity. Its fishing port has a narrow entrance that limits exchange of seawater between the bay and open ocean, allowing the accumulation of fine-grained precipitates of iron-bearing materials (Fe-oxyhydroxides) on the seafloor. The fishing port is usually filled with orange- to brown-colored Fe-rich water, and deposits >1.5 m thick Fe-rich sediments. To elucidate the movement and depositional processes of the Fe-rich precipitates in the bay, we conducted continuous profiling of turbidity throughout the tidal cycle and monitoring of surface water. The results showed that clear seawater entered the bay during the rising tide, and turbid colored water flowed into the ocean during the ebb tide. Neap tide was found to be an optimal condition for sedimentation of Fe-oxyhydroxides due to weak tidal currents. Storms and heavy rains were also found to have influenced precipitation of Fe-oxyhydroxides. Storm waves disturbed the bottom sediments, resulting in increased turbidity and rapid re-deposition of Fe-oxyhydroxides with an upward-fining sequence. Heavy rain carried Fe-oxyhydroxides originally accumulated in nearby beach sands to the bay. Our findings provide information on optimal conditions for the accumulation of Fe-rich sediments in shallow-marine hydrothermal settings.