The local marine environment is extraordinarily diverse. The islands of the San Juan Archipelago provide an enormous array of rocky outcroppings, protected lagoons, high energy intertidal beaches and extensive mudflats. The channels and straits of the region provide muddy, rocky and sandy flats, as well as trenches of depths up to 100 m. This diversity of habitat obviously provides for a very rich and diverse biota. There are several gull rookeries nearby and owls, hawks and bald eagles are frequently seen.
Harbor seals are common and killer and gray whales are occasionally seen nearby.
The nearby Padilla Bay National Estuarine Research Reserve is only one of many protected coastal areas that can accommodate long-term research projects. Some 900 m of cobble beach and intertidal extending to 65 m seaward from mean low-water at SPMC is under State protection. This area contains muddy and cobble bottom, shellfish beds, and extensive algal communities. Research is facilitated by ready access to the adjacent laboratory and on-site access to electrical power. Local estuaries occur on small spatial scales, providing rapid transition from fresh to saline water.