The lagoons are resting areas for migratory waterfowl using the Pacific Flyway between Lake Earl on the Smith River estuarine wetlands 40 miles (64 km) to the north and Humboldt Bay on the Mad River estuarine wetlands 30 miles (48 km) to the south.

Stone Lagoon is similar to other coastal features of northern California including Humboldt Bay to the south and Lake Earl to the north.

Hills adjacent to Stone Lagoon have been identified as undivided pre-Cretaceous metasedimentary rock.

[1] Studies around Humboldt Bay indicate tectonic activity along the Cascadia subduction zone has caused local sea level changes at intervals of several centuries.

A restaurant, service station, and motor lodge were built between the highway and the lagoon in 1927.