We investigated the distribution of benthic foraminifera in Lake Saroma, a large lagoon on the coast of the Sea of Okhotsk in Hokkaido, Japan, to establish the characteristics of the foraminiferal fauna in these cool, organic-rich, brackish-water environments. Three types of faunas were identified: a Lagoon-bottom fauna dominated by Haynesina sp. A, a Shallow-water fauna dominated by Trochammina cf. japonica, and a River-mouth fauna dominated by Elphidium excavatum. The distribution of species is controlled by the dissolved oxygen content of bottom water in the summer, and a combination of organic enrichment and high mud content in the substrate that is specific to areas off river mouths. Haynesina sp. A opportunistically adapts to organic-rich and oxygen-poor conditions in deeper basins in the lagoon during the summer, whereas Trochammina cf. japonica mostly occurs in shallower areas where summer oxygen levels are high enough to sustain reproduction. Elphidium excavatum probably adapts to organic-rich sediments specific to areas near river mouths.