Secrets to An Unforgettable San Juan Island Adventure
August 15, 2022
A Bite of Mexico on Lopez Island
September 25, 2022
Sea Lion by Jess Newley

This Steller sea lion is just one of the unique wildlife encounters that you can enjoy while visiting the islands. Keep an eye out for large colonies hauled out on rocks and an ear out for their roars often heard throughout the night. Credit: Jess Newley

Beneath the Sea

Exploring the Wonders Under the Surface of the San Juan Islands

By Jess Newley


Breaching killer whales, soaring eagles, swimming sea lions, and stunning shorelines

Breaching killer whales, soaring eagles, swimming sea lions, and stunning shorelines

Breaching killer whales, soaring eagles, swimming sea lions, and stunning shorelines—these are just a few of the sights that people travel to the San Juan Islands every year by foot, boat, or plane to behold. If you’ve been to the islands before, then you know that their moniker as “the hidden gem of Washington State” is true. But did you know that under the water there is a whole system of wondrous natural resources (eelgrass, kelp, forage fish, juvenile salmon, and of course, killer whales, to name a few) that support what we get to experience above the surface?

Residents and visitors alike play an important role in stewarding the marine habitats of the Salish Sea. Read on to learn more about a few vital habitats and species of this region, and how you can help support and maintain them.

Eelgrass is a flowing plant that grows in shallow, light-filled marine waters. Eelgrass forms large meadows of underwater vegetation that support marine food webs. At low tide, it is easy to see eelgrass, especially in the spring and summer when it thrives. Eelgrass abundance varies seasonally with some winter die-off. The long blades of eelgrass are an underwater nursery for incubating eggs, such as herring, and provide food and refuge for a wide array of small creatures and young animals, including Dungeness crab, juvenile flatfish, and salmon. Eelgrass beds are also important feeding areas for birds. In addition, eelgrass mitigates wave energy and traps sediments, safeguarding shorelines from wave-driven erosion.

If you are a boater, you can help protect eelgrass by anchoring in water deeper than 30 feet. While each individual anchor might create just a small scar in the meadow, the cumulative effects can be dramatic enough to be seen in satellite images from space. To avoid damaging eelgrass, it’s best to use a public marina or mooring buoy. When those options are not available, anchor deeper than 15 feet at low tide in bays, and in more than 30 feet of water in more open areas. You can explore an eelgrass depth map at and see for yourself where eelgrass is growing around the islands. Lastly, avoid chemicals when cleaning your boat and if you live near the shoreline, limit the use of lawn and garden chemicals.

Kelp needs clean water and light to thrive. It is very sensitive to pollution from small and large oil spills, soil erosion, and yard chemicals. If you live near the shoreline and have a septic system, you can help by making sure your septic system is working properly and reducing your use of chemicals. If you are a boater, keep your boat in good condition, and clean even the smallest of fuel spills using absorbent pads—not soap. And of course, for your safety, and for the kelp, always steer clear of kelp beds when underway.

Forage fish, or bait fish, are small schooling fish that are eaten by larger fish, seabirds, and marine mammals. Primary species in the Salish Sea are Pacific herring, Pacific sand lance, and surf smelt. Each of these forage fish plays an essential role in marine food webs by transferring energy from plankton to larger species. Forage fish are staples in the diets of fish, seabirds, and marine mammals, including chinook and coho salmon, lingcod, Marbled Murrelets, Rhinoceros Auklets, and Minke whales.


Forage fish do not spawn just anywhere. Pacific herring deposit transparent, adhesive eggs on eelgrass and marine algae close to shore. Surf smelt and Pacific sand lance incubate their eggs on beach sand and small gravel near the high tide line. These spawning forage fish utilize the same shoreline areas that we humans also concentrate our activities on, making them vulnerable to shoreline alterations such as armoring or bulkheads, docks, roads, and the removal of vegetation. You can help forage fish by keeping beaches natural with plenty of overhanging native trees and shrubs. Large driftwood is also beneficial as it helps to maintain cool and moist conditions for the tiny eggs.

You don’t get to visit or live in Washington State without hearing about salmon. These fish are the lifeline to indigenous cultures, economic stability, ecosystem functionality, and so much more. Did you know that the San Juans are an important rearing habitat for juvenile salmon? Each spring and summer young salmon, just inches long, migrate from their natal rivers across the Salish Sea through the productive shoreline habitats of the islands. This is a critical time for young salmon as researchers have found that the amount of time juvenile salmon spend in the marine nearshore, eating and growing as fast as they can, is critical to their ability to survive as adults.

Marine mammals such as Southern Resident killer whales depend on adult salmon for food when these anadromous fish pass back through the San Juans on their way to spawn in their natal rivers. Salmon are also culturally vital to Northwest Tribes. Perhaps you appreciate feeding on salmon too.

To help salmon, avoid single use plastics that often make their way into rivers and marine waters. You can also help by protecting eelgrass and kelps where the tiny fish hide and find forage fish to eat. If you are a waterfront property owner there is so much you can do to help salmon. Did you know that juvenile salmon eat insects that fall into the water from shoreline vegetation? By keeping your beach free of shoreline modifications and retaining overhanging vegetation, detritus and driftwood, you will support the insects and forage fish that young salmon eat. Also, juvenile salmon tend to avoid swimming under docks, and instead move out into the deeper waters where they are at risk from predators. To reduce demand for new docks, consider using a marina, mooring buoy, or sharing an existing dock with neighbors. If you already have a dock, look into improvements that can increase light penetration such as grating.

We have two distinct killer whale populations swimming through Salish Sea waters and the San Juan Islands. The most well-known is the Southern Resident killer whales whose diet consists of fish, primarily salmon. We also have transient killer whales (aka Bigg’s killer whales), who eat marine mammals like harbor porpoises, seals, and sea lions. Recently, transient killer whales are thriving in the Salish Sea with plenty of harbor porpoises, seals, and sea lions to eat. More often than not there is a family of transients swimming somewhere between the islands and chances are high that you will get to see them.      

Southern Resident killer whales are an endangered species that used to regularly spend their summers in the region but are visiting the islands less. Southern Residents depend primarily on a diet of chinook salmon. Southern Residents need space and quiet waters to find this limited food. Luckily there are many places in the San Juans to view these very special species from shore. Consider joining the regional Give Them Space movement to avoid watching Southern Residents from vessels. Instead, focus on the exciting Bigg’s whales or view the whales from shore at Lime Kiln State Park next time you’re on San Juan Island. If you end up boating near the Southern Residents, make sure and stay at least 400 yards away. Visit for more information and viewing guidelines.

Salmon, eelgrass, bull kelp, forage fish, and orcas—all of these wondrous things are connected in ways that we don’t always see or experience as humans living above the surface of the Salish Sea. If we lose one of these important pieces of the puzzle, the Salish Sea and all who rely upon it will suffer. It is more and more important that we all do our part to take care of this special place and do what we can to protect it for people and nature.

Next time you are looking out the ferry window, off the aft of a boat, or gazing from a plane as you fly over, take a moment and go deeper. Remember that this amazing and complex web of life, that exists outside of our normal view, depends on all of us to steward and to protect it.    

Get There with a Scenic Flight

If you’re already aboard a Kenmore Air flight, this may be old news. But getting to the San Juans doesn’t have to be a slog. In fact, the scenic flight can be half the fun!