The tsunami following the Great East Japan Earthquake in March 2011 resulted in significant ground subsidence and deposition of rubble and mud in the Natori River, near the city of Sendai (Miyagi Prefecture), damaging its brackish water ecosystem and fishing grounds. There was a direct impact in the form of annihilation of animal and plant life and disturbance of the habitats throughout. Also, a wedge of seawater ran far upstream, and ground subsidence changed the pattern of tidal flow in the river. Brackish water ecosystems such as that near the mouth of the Natori River are important as nurseries for juvenile fishes and as a fishing ground for bivalves such as clams. The populations of both of these kinds of organism declined drastically as result of the tsunami. The catch per unit effort of ayu fish (sweetfish; Plecoglossus altivelis altivelis) in 2011 was the lowest recorded for the past 5 years, and the population hatching date composition showed a marked absence of early-hatched individuals. In contrast, the residual upstream ayu fish population seems to have grown successfully and reproduced despite the effects of the tsunami: 1 year after the tsunami occurred, the downstream ayu fish population had recovered to the same level as before the event. However, the population of the brackish-water clam, Corbicula japonica, only showed recovery 2 years after the disaster as its habitat has drastically shifted due to movement of the brackish water zone about 1 km upstream. The studies reported here show that the impact of the earthquake and tsunami on pelagic fish and benthic bivalves seems to have been quite different, as in the former recovery was rapid, while in the latter it took much longer. Many other fish species also returned to normal levels within a year, such as stone flounder (Kareius bicoloratus), goby (Acanthogobius lactipes), icefish (Salangichthys microdon) and black porgy (Acanthopagrus schlegelii). The food web structure appears to be slightly different from past years, but the results show that, in general, fish communities are able to recover rapidly from disturbances even as drastic as an unusually large tsunami.