Gamo Lagoon (Sendai, Miyagi Prefecture, Japan), a shallow brackish lagoon, was struck by a 7.2-m-high tsunami on 11 March 2011. In order to assess the tsunami-induced changes in the ecosystem of Gamo Lagoon, we examined the topography and distribution of plants and macrobenthos between April and August, 2011, and compared them with available pre-tsunami data. The submerged area decreased from 17.3 to 11.8 ha, sand dune vegetation from 8.6 to 0.1 ha, pine forest from 4.2 to 2.0 ha, and macroalgal patches from 7.8 to 1.8 ha. Conversely, the area of bare intertidal flats increased from 4.7 to 5.3 ha, mainly owing to the near disappearance of reed marshes (7.8 to 1.2 ha). Muddy sediment was flushed out and the sediment became sandier. The population of the marsh-associated gastropod Cerithidea rhizophorarum in the lagoon declined sharply from about 40,000 (estimated from mean density and habitat area) to just 26 individuals. Of 79 species of macrobenthos found before the tsunami, 47 species (especially bivalves) were absent or nearly extirpated after the tsunami. The temporary immigration of 12 marine species was noted shortly after the tsunami, but most disappeared within 5 months. The populations of dotillid crabs (i.e., Scopimera globosa and Ilyoplax pusilla), the nereidid polychaete Hediste diadroma, and opportunistic species including polychaetes (e.g., Pseudopolydora cf. kempi, Heteromastus cf. similis, and Capitella sp.) and amphipods (Grandidierella japonica and Corophiidae sp.) recovered rapidly within the same 5-month period.