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Two Day San Juan Island Kayaking Tours: Kayak in Orca Whale Waters

Why Choose Sea Quest for your Two Day Kayak Tour in the San Juan Islands?

  • Bull Orca Fin cuts past Kayak Tour off San Juan IslandLowest priced kayak tours to the prime killer whale zone where most whale sightings occur.
  • Kayak the stunning seashores & lighthouses of the wilder western San Juan Islands.
  • Best route to kayak with killer whales in the US with 470+ orcas from spring through autumn.
  • Camping on small islands with abundant eagles, otters & seals. Routes include a National Monument, National Wildlife Refuge, State & County Parks, and possibly a National Historical Park.
  • Our campany has been leading kayak tours in the San Juan Islands since 1989 with a perfect safety record thanks to extensively trained guides and the newest kayaks & paddling gear.

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Two Day San Juan Islands Sea Kayaking Tours

Our two-day sea kayak trips in the San Juan Islands are the perfect choice if you have limited vacation time or want an introduction to camping where rain is a rare event. The gorgeous snow-capped Olympic Mountains are more than mere scenery on this kayak tour – they make the San Juans the driest micro-climate along the Washington coast. Tiny cactus and red-barked madronas cling to steep sea cliffs thanks to the Mediterranean climate. Elsewhere, dense forests of massive dark green firs cloak the landscape. Below the surface, forests of multi-colored kelp wave rhythmically in the strong currents that bring nourishment to sea stars and diverse tidepool life.

Blood Stars live in the Colorful Tidepools of San Juan IslandWe have had excellent success in kayaking with orca whales on this kayak adventure. Our route traverses the ultimate killer whale habitat on both days of the two-day kayak tour. From 2005-2018 we encountered orca whales on about 40% of the trips in May, 50% in June through September, and 30% in October. Amazingly, this span began in the same year our salmon orcas were listed as endangered! Before 2005, salmon orcas and their prey were thriving and we saw them even more often. Sadly, the salmon have dwindled, leading to two terrible years for killer whale watching in 2013 and 2019. Clearly, the future of whale watching is now unpredictable and we can only hope that humanity is willing to make the changes necessary to ensure abundant salmon and orcas in the years ahead.

The San Juan Islands remain the best place in the US for seeing killer whales, despite erratic results in recent years. Sea Quest’s many decades of experience, both as local biologists and expert kayak guides, provides you the best chance to see these spectacular whales! While the salmon orca struggle to find prey, a newly recognized species of killer whale shares Washington’s waterways. Bigg’s killer whales hunt marine mammals and are thriving on our growing population of harbor seals and sea lions. They number over 400 individuals but are quiet, stealthy, and difficult to locate compared to salmon orcas.

In addition to killer whales, many other exciting marine mammals may be seen: humpback whales, minke whales, harbor and Dall’s porpoise, mink and river otters. Peregrine falcon eyries, bald eagle nests, a pelagic cormorant rookery, colonies of guillemots, breeding black oystercatchers and kingfishers are just some of the avian features. This kayak tour is also available as a Women’s-Only Kayaking Vacation.

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Trip Details: Two-Day Kayak Tour from San Juan Island

  • Schedule: weekends Saturday-Sunday.
  • Trip Fee: $399 plus $10 county launch tax.
  • Meeting Time & Place: Early morning Friday Harbor, San Juan Island – your email confirmation provides the exact time but you will be able to arrive via ferry in time. Look for our van and kayak trailer in the traffic circle adjacent to the Friday Harbor Ferry Terminal.
  • Day 1 Itinerary: We go straight to the launch beach, load the kayaks, and then prepare everyone with the basic skills during a hour-long instructional session. We launch directly into prime orca whale watching territory and must keep a sharp eye out for “blows” as we paddle. Our route passes numerous islets, rocks, and reefs rich in wildlife. Paddling time may vary from 4 to 6 hours, covering 8 to 12 miles each day depending on sea conditions. To keep fresh, we take several floating rest stops throughout the day, plus one or more visits ashore for lunch and relaxation. We will spend the night at a spectacular marine park. After dinner you can request a moonlight paddle and may see bioluminescent life swirling in the waters like fairy dust.
  • Day 2 Itinerary: After enjoying the morning sunrise, we break camp and launch for another wonderful day of sea kayaking. We cover a similar distance as the day before, still sticking to the main thoroughfares of killer whales. After landing we reboard the van.
  • Finish Time & Place: Friday Harbor Ferry Terminal between 1:00 and 3:00pm. This allows you time to catch various departing ferries if you desire to leave the island that evening.

Sea Quest Kayak Expeditions Provides:
All sea kayaking trip gear, transportation from Friday Harbor to the launch beach, instruction and knowledgeable guides.
You Will Provide:
Outdoor clothing, wet footgear, lunch, beverage, hat, sunglasses, and sunscreen. Click prepare for a San Juan Islands kayak tour for more info.

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Two-Day San Juan Islands Kayaking Tours Map:

  • The green shaded area is the main orca whale feeding and traveling route. We stick very closely to the killer whale waters on both days of our two-day kayaking tour. The red lines represent the most frequent routes we use but by no means depict the exact route your tour will follow.
  • The primary or “North” route travels north from the west side of San Juan Island through a top killer whale watching corridor. The campsite is most often Stuart or Posey Islands. From Stuart Island we may attempt a sunset or dawn hike to a clifftop lighthouse that overlooks a great whale watching point. Weather and currents must be cooperative and the group must be moderately fit to reach Stuart. On some days, regardless of fitness, conditions will mandate camping on Posey Island, a tiny jewel included in the National Monument.
  • The “South” route begins at San Juan Island National Historical Park at the south end of San Juan Island. Killer whale watching is excellent here, too. Especially on the Salmon Bank that extends from the picturesque Cattle Point Lighthouse. The largest concentrations of baitfish and salmon occur here and attract orcas, minke whales, porpoises, seals and sea lions. Orca pods and minke whales visit almost daily and may make repeated visits in a single day. We may decide to operate your tour on this route depending on a variety of factors, including availability of campsites, recent patterns of whale sightings, anticipated weather, and the predicted power and direction of tidal currents.  We will certainly use this route on several trips, but usually don’t make the determination until too late to provide notice. Rarely, we may know in advance and will post the dates here. They will be labeled in the online reservation system as “South Route”.
  • The “West” route is the absolute best for orca whale watching encounters with the highest chance of sightings. From our launch beach at San Juan County Park on San Juan Island, we explore south to Lime Kiln Park and beyond, and north to Henry Island. This should be the least physically demanding route, but the most productive for killer whale sightings. The trade-off is that we camp at our launch beach on San Juan Island and will not visit the “wilder” parts of the archipelago. There are no confirmed dates in 2020 but will likely be available again in 2021. These dates are labeled in our online reservation system “West Route”.
  • Please note: The green-shaded area can experience extreme winds or currents even in summer. This can occasionally cause us to reduce our intended time within, or avoid entirely, the primary orca watching zone as safety is the top priority. In these situations we always have opportunities to watch for whales from trails or beaches that overlook the the best areas.

Click the map below to open a full-size chart in PDF format that you can save, zoom, or print!

2 Day San Juan Islands Kayaking Tour Map

Internationally Renowned Sea Kayaking

Kayaking with Killer Whales on a Two Day San Juan Island Kayak Tour


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