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

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

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

The relatively small catchment basin tributary to Freshwater Lagoon has allowed formation of a durable coastal sand bar which has not been breached by recent storm events.

There is also a Redwood National and State Parks visitor center near the north end of the lagoon.