The 2011 tsunami in Japan severely disturbed the benthic biota in Matsushima Bay (Miyagi Prefecture) via sediment erosion. Eelgrass beds markedly decreased from their original coverage of 2.2 km2 in June 2007–0.02 km2 in May 2012. Although our monitoring indicates that the eelgrass beds are slowly recovering, an analysis based on a Habitat Suitability Index model suggests that their recovery is restricted by deteriorated light conditions due to land subsidence resulting from the prior earthquake. Additionally, the tsunami severely damaged a sewage treatment plant adjacent to the bay, and this led to acute increases in chemical oxygen demand and coliform bacteria in the seawater. However, the water quality improved when the damaged sewage treatment plant started temporary operations, such as sedimentation, aeration, and chlorination, and recovered to pre-tsunami conditions in approximately 1.5 years. These results demonstrate that temporary treatment methods are important to minimize acute impacts of treatment facility damage on water environments.