A Guide to Wildlife in the San Juan Islands

Did you know the San Juan Islands are home to one of the most diverse ecosystems in the entire world? It’s true!


Every time we set out on a whale watching tour by boat, our number one goal is to see whales. Most days we do, but we also see a huge variety of other wildlife, including animals many of our guests have never seen up close before! Our kayak tours encounter a variety of diverse wildlife, and sometimes whales, too!


If you ever join us on one of our unforgettable tours in Friday Harbor or Roche Harbor, here’s a preview of some of the exciting wildlife you might encounter:


Everyone wants to see whales, and it’s easy to understand why. They’re elegant, majestic animals, and seeing them in the wild is just plain amazing!


Orcas (“Killer Whales”)


Orca whales (a.k.a. killer whales) are the largest of the dolphin species. Orcas are known for being curious and intelligent. They’re also excellent predators, but not all orcas are after the same prey.


There are two distinct genotypes of orcas in the Puget Sound:

Resident Orcas

  • Eat fish

  • Travel in large, socially complex pods, each lead by a matriarch

  • Stay with the same pod for life, making each pod a cohesive family group

Transient Orcas

  • Eat mammals like seals, porpoise, and occasionally gray or humpback whales

  • Travel in small pods of 3-5

  • Have a broad range of travel from California to Alaska


Read more about orca whales.

Baleen Whales

We often see baleen whales in the San Juan Islands too! Baleen whales are a group of species that includes humpback, gray, and minke whales.


Humpback Whale


Humpback whales can grow to 52 feet and often feed in the Puget Sound area during the fall before traveling to tropical waters for the winter. Humpback whales are famous for the amazingly complex song that the males sing. In 2015 alone, approximately 50 different humpback whales were sighted in the Salish Sea, and more are expected to travel through every year!


Gray Whale


Gray whales are a little smaller, only growing up to 45 feet. They have the longest annual migration route of any mammal (10,000 to 12,000 miles a year!).

Minke Whale


Minke whales only average about 30 feet in length. There are about 17 minke whales in the waters surrounding the San Juan Islands, but that doesn’t mean we never see them! They love traveling in groups and eating schooling fish during summer months.


Did you know? The word “baleen” actually refers to the filter-feeder system that these whales have inside their mouths. Baleen is similar to bristles, but it’s made out of keratin, like human hair and nails. Baleen whales catch food by taking in water through their mouths and trapping crustacean, fish, and krill in their baleen plate.


A humpback whale with a visible baleen plate



Bird lovers have a blast on our tours! We’ve seen so many amazing species up close, including bald eagles, hooded mergansers, both double-crested and pelagic cormorants, common murres, tufted puffins, and rhinoceros auklets. We also see harlequin ducks, herring gulls, pigeon guillemots, both Pacific and common loons, great blue herons, and so many more that there’s not space to list them!


In fact, there are so many birds to see in the San Juans that we offer special Birding Safaris. Most birds enjoy being on or around our waters during fall, winter, and spring. Many have already migrated by summer, but some stick around.

Seals & Sea Lions


We love seeing seals and sea lions whenever we get the chance, and we see quite a bit of both.


Many people ask us: What is the difference between seals and sea lions? They’re closely related, but it’s easy to tell them apart once you know what to look for:


Sea lions are big and brown and have large flippers they use to “walk” on land. Seals are smaller, have small flippers, and move around on land by wriggling on their bellies. Sea lions also have visible ear flaps, which seals don’t have. Another difference? Sea lions are loud! They can make a noisy barking sound to communicate and interact with each other.

Dall’s Porpoises


The Dall’s porpoise is a small black and white marine mammal. Its colors can make it easy to mistake for an orca from afar, but Dall’s porpoises are shaped differently, with thick bodies and small heads.


We’ve also been known to see harbor porpoises in the waters surrounding the San Juan Islands. Harbor porpoises are a little smaller and usually gray in color.


Like killer whales and dolphins, porpoises are very intelligent and social, often traveling in groups.

Starfish, Jellyfish, and Other Invertebrate Sea Life


If you look closely enough, you’re also likely to see a huge variety of smaller sea life in the waters around the San Juan Islands too. Starfish are always a treat, and we see many different kinds of jellyfish, including:


  • Moon jellyfish: Beautiful, with an opaque white color and a very mild sting

  • Water jellyfish: Almost completely transparent with lines running along their bells

  • Lion’s mane jellyfish: Large and brilliantly maroon with a powerful sting

  • Fried egg jellyfish: Look just like an egg with a white bell and yellow internal organs

So Much More

The waters surrounding the San Juan Islands truly are a one-of-a-kind ecosystem. This guide just scratches the surface of all the amazing animals we see. For example, we often see families of river otters swimming around near our tours.


That’s why each of our tour groups is accompanied by a marine naturalist. Our naturalists are enthusiastic, passionate, and extremely knowledgeable. They make sure all guests have the time of their lives! Plus, more than 95% of our vessel tour groups see whales!



With San Juan Outfitters, you have the option of getting down in the water with these amazing creatures in a kayak, or enjoying the unforgettable experience from the comfort of one of our Coast Guard approved vessels.


Book your trip now, or call (866) 810-1483 and ask us your questions. We hope to see you on the water soon!

Photo credits: Phalacrocorax pelagicusCC BY 2.0Gray whale spyhopping 6CC BY 2.0

December 20, 2016