Since the two devastating tsunamis in 2004 (Indian Ocean) and 2011 (Great East Japan), new findings have emerged on the relationship between tsunami characteristics and damage in terms of fragility functions. Human loss and damage to buildings and infrastructures are the primary target of recovery and reconstruction; thus, such relationships for offshore properties and marine ecosystems remain unclear. To overcome this lack of knowledge, this study used the available data from two possible target areas (Mangokuura Lake and Matsushima Bay) from the 2011 Japan tsunami. This study has three main components: (1) reproduction of the 2011 tsunami, (2) damage investigation, and (3) fragility function development. First, the source models of the 2011 tsunami were verified and adjusted to reproduce the tsunami characteristics in the target areas. Second, the damage ratio (complete damage) of the aquaculture raft and eelgrass was investigated using satellite images taken before and after the 2011 tsunami through visual inspection and binarization. Third, the tsunami fragility functions were developed using the relationship between the simulated tsunami characteristics and the estimated damage ratio. Based on the statistical analysis results, fragility functions were developed for Mangokuura Lake, and the flow velocity was the main contributor to the damage instead of the wave amplitude. For example, the damage ratio above 0.9 was found to be equal to the maximum flow velocities of 1.3 m s-1 (aquaculture raft) and 3.0 m s-1 (eelgrass). This finding is consistent with the previously proposed damage criterion of 1 m s-1 for the aquaculture raft. This study is the first step in the development of damage assessment and planning for marine products and environmental factors to mitigate the effects of future tsunamis.