We conducted a 5-year monitoring survey of a population of Eisenia bicyclis kelp at a coastal area that suffered subsidence from the 2011 earthquake and the subsequent breakwater restoration work. Due to subsidence, the former intertidal area sank to the subtidal zone, therefore, the density of E. bicyclis increased because of many recruits. However, after the restoration work, the area harboring the recruits was destroyed and landfilled. In an area that sank below the pre-subsidence border of the kelp distribution, recruits were rare. Furthermore, an indirect effect of the restoration work was also observed on recruitment in the intact offshore kelp zone. Our results showed that the breakwater restoration work following subsidence had negative effects, not only to the density but also to the age structure of the E. bicyclis population.