Three Day San Juan Island Kayak Trips: Kayaking in Orca Whale Waters

Why Choose Sea Quest for your Three Day Kayak Trip in the San Juan Islands?

Bull Orca Spyhops in the middle of a Sea Quest Kayak Tour

  • Best route for kayaking with orca whales in the entire US – home to over 470 killer whales.
  • Lowest priced kayak trips to the top orca whale watching habitat where virtually all sightings occur in the San Juan Islands.
  • Routes combine a National Wildlife Refuge, a National Monument, several State & County Parks, and often a National Historical Park!
  • Camp on small islands with abundant harbor seals, otters & bald eagles.
  • Kayak the beautiful sea cliffs & lighthouses of the western San Juan Islands along the border with Canada.
  • We have led kayak tours in the San Juan Islands since 1989 and have a perfect safety record.
  • The best trained biologist/naturalist guides and the newest state-of-the-art kayaks & and paddling equipment.

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Three-Day San Juan Islands Sea Kayaking Tours

Our three-day kayak tours in the San Juan Islands are our most popular camping trip. Extremely dry summer weather, whales and wildlife, and hundreds of intricate islands unite to make this the ultimate sea kayaking trip and camping adventure, especially for first-timers. If you enjoy relaxing to starry skies and meteorite showers, and revel in the beauty of sunrises and sunsets, this three-day kayaking adventure in the San Juan Islands is for you!

Kayak Tour on San Juan Island Beach The three-day San Juan Islands kayaking trip is similar to our two-day kayak trip, but having an extra day sandwiched in the middle imparts a much more relaxed feel to the experience. It may not seem significant, but we notice our guests really unwind on that middle day, beginning with the dawn chorus of songbirds and ending with the hooting of owls at bedtime. For one day at least, you won’t have to think about planes, ferries, and automobiles. The three-day kayak trip in the San Juans is a great escape from modern stress.

Killer whale watching is possible on this kayak camping adventure in the San Juan Islands. Each extra day in the killer whale watching zone improves your chances of seeing orcas and other interesting wildlife. From 2005-2018 our guests watched orcas on 30% of the 3-day tours in May, 70% in June, 60% in July, 55% in August, 55% in September, and 35% in October. Surprisingly, salmon and salmon orcas have both been listed as endangered throughout those years! Prior to 2005 we found whales even more often because salmon were still abundant in that earlier era. Environmental conditions have taken a turn for the worse and very few salmon migrated through the San Juan Islands in 2013, 2019, and 2020. Very few salmon orca were sighted in those three years, underscoring the fact that whale-watching will be much less predictable until our society takes the necessary steps to recover salmon spawning habitat.

The San Juan Islands remain the best place in the US to watch killer whales. While salmon orca struggle to find food, a related species known as Bigg’s killer whale is finding plenty of prey and their population has grown to over 400 in our region. Fortunately for them, they specialize in hunting our expanding herds of seals and sea lions. This requires them to travel in smaller pods and be much stealthier than salmon orcas. Even though they are not endangered, spotting them on our kayak tours can be very challenging compared to the salmon orca. Learn more about kayaking with killer whales with Sea Quest here.

Read our two-day kayak trip description to learn more about features common to all of our camping tours. This kayak trip is also available as a Women’s-Only Kayaking Vacation.

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Trip Details: Three-Day San Juan Island Kayak Tour

  • Schedule: Tuesday-Thursday & Friday-Sunday with some exceptions for holidays.
  • Trip Fee: $699 plus $10 government launch tax/fee.
  • 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 direct to the launch site, ready the kayaks, and spend the next full hour in basic skills and safety instruction. Paddling begins in the prime killer whale watching zone and throughout the next three days we can spot them at any and all times. The entire route is excellent wildlife habitat sprinkled with reefs, rocks, and islets. Kayaking time ranges from 4 to 6 hours daily, traversing 8 to 12 miles per day in typical weather. Paddling is punctuated by one or more beach landings and numerous float breaks at interesting places each day. Marine parks serve as campsites. Post-dinner we may hike to a viewpoint, do a short sunset or moonlight paddle, or stroll the shore in hopes of seeing bioluminescent plankton.
  • Day 2 Itinerary: Sunrise wakeup, breakfast made fresh by your guide, then a carefree day of exploration in our sea kayaks. Again we’ll travel through important killer whale and porpoise habitat. There are many beautiful sights along the way, including views of three mountain ranges: the Olympics, North Cascades, and Coast Range. Several route options exist with the guide’s decision determined by expected currents, weather forecasts, and group ability and interests. If the paddling day is short, we often hike 5 miles round trip to a picturesque lighthouse perched high on a headland with stunning views. The vantage is perfect for spotting whales and porpoises or watching the sun set. As the sun approaches the horizon, it paints the glassy waters in outrageous colors.
  • Day 3 Itinerary: After enjoying the morning sunrise, we breakfast and depart for another wonderful day of sea kayaking. As always, we stick close to the main thoroughfares of killer whales. After landing we reboard the van for the drive to Friday Harbor.
  • 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 Tours 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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Three-Day San Juan Islands Kayak Trips Map:

  • The orca whale’s top hunting and traveling areas are shown as shaded areas. We kayak in the primary killer whale watching zones for both species of killer whales for the majority of the tour. The red lines show our typical routes but do not indicate the exact route you may experience.
  • The main or “North” route explores north from the west side of San Juan Island through an important orca whale watching corridor. Stuart and Posey Islands State Parks are the campsites most frequented. Stuart Island features a hike to a clifftop lighthouse known for excellent whale watching. The group must be moderately fit and sea conditions must be safe to reach Stuart Island but we make it on nearly all trips using the northern route. If the situation dictates, most often by strongly opposing tidal currents, we camp on tiny Posey Island, a part of the National Monument. Rarely, strong adverse currents have required us to camp at San Juan County Park on San Juan Island for a night, with an exploration of the Lime Kiln Whale Watch Park. This campsite boosts our chances of spotting whales a bit higher and are labeled “SJCP” or “Strong Currents” in the online reservation system. No trips are planned to camp at San Juan County Park in 2021 so far.
  • The alternate or “South” route launches from the south end of San Juan Island at the National Historical Park. Orca whale watching is fantastic on the Salmon Bank, a shallow bar connecting to Cattle Point Lighthouse. Dense schools of baitfish draw in hungry salmon, minke whales, porpoises, sea lions and seals. Killer whales and minke whales are frequent visitors, sometimes making multiple daily forays. Our decision to use the southern kayak route is influenced by recent whale activity, weather forecasts, and campsite availability in the San Juan Islands. 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”.
  • A note about currents: Tidal currents are very strong at certain times and switch direction four times each day. Our goal is to travel with the currents but this is not possible at all times. Opposing currents could result in arriving at destinations an hour or two later than normal, or cause other spontaneous variations in the itinerary. Our online reservation system will display those dates as “Strong Currents”. You may wish to avoid these dates if you are not physically fit or an experienced paddler as they may present a greater challenge. Occasionally, we avoid adverse currents by using the South route, or a hybrid route combination of the South/West/North routes (that may include a camping night at San Juan County Park). These will all be uniquely labeled in our reservation system.
  • Be aware: The shaded zones can be unsafe for kayaking if strong solar-induced winds or unseasonable weather fronts occur. On occasion, we may have to curtail our planned time or even forgo paddling in the main killer whale watching areas. Safety always takes priority over whale watching. If weathered out we will attempt to scan for whales from good shore locations.

Click the chart below if you want to see zoom in for more detail or print a copy!

Internationally Renowned Sea Kayaking

Your Best Chance to Kayak with Orca Whales
on a Three Day San Juan Island Kayak Trip

Join a Kayak Quest for Whales Today! Call 360.378.5767 Address: By appointment only: 322 Daniel Lane, Friday Harbor, WA 98250 ©2022 Sea Quest Kayak Tours / Natura LLC, All rights reserved. Privacy Policy