San Juan Sea Kayaking



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 / Historic Park and several State & County Parks

Camp on small islands with abundant seals, otters & eagles.

Kayak the beautiful sea cliffs & lighthouses of the western San Juan Islands along the border with Canada.

Perfect safety record since 1989 on all San Juan kayak tours.

The best trained biologist/naturalist guides and the newest state-of-the-art kayaks & and paddling equipment.

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Ready to Start Your Adventure?

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!

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 struggles to find food, a related species known as Bigg’s killer whale find plenty of prey, and their population has grown to over 400 in our region. Fortunately, 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 our camping tours. This kayak trip is also available as a Women’s-Only Kayaking Vacation.

Trip Details: Three-Day San Juan Island Kayak Tour


3 Days

Group Size

All Group Sizes

Age Range

All Ages

Activity Level


Starting From



8:00am Every Day


San Juan Islands, WA

RATED 4.7/5

(912 Reviews)

  • Schedule: Tuesday-Thursday & Friday-Sunday with some exceptions for holidays.
  • Trip Fee: $849 plus $10 government launch fee.
  • Meeting Place: Friday Harbor, San Juan Island. Look for our van and kayak trailer in the traffic circle adjacent to the Friday Harbor Ferry Terminal.
  • Meeting Time: 8:00am. On some dates there may be a slight difference in trip start time. Our online reservation system will indicate this if you enter a specific date. Ask about earlier or later departures if the starting times shown don’t work for you!
  • 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.


Frequently Asked Questions​


Our most popular kayak camping tour length is our three day kayak camping tour. It is our most commonly attended tour for the following reasons: Adventure Value + Tour Duration: A three day tour allow you to access remote islands in the San Juan Archipelago and still allows you freedom and flexibility in your schedule for other vacation activities. This tour packs a punch! Time for Relaxation: We often find our guests love having a day in the middle of their tour where they don’t have to think about any travel logistics whatsoever and can fully immerse themselves in their natural surroundings. Access to a Diversity of Wildlife: Three days is a long enough period of time to view a range of different wildlife in different habitats. You will be amazed at what you can see over the course of a kayak tour with Sea Quest.

Anyone in moderate physical condition can join a three day kayak camping tour. While most people do have some prior experience in small boats or camping these experiences are not necessary.

If you would like to prepare for your tour we recommend a mixture of walking, cycling, swimming and of course paddling! You can also prepare by focusing on core and upper body exercises.

A three day kayak camping tour offer many islands to explore in the San Juan Island archipelago. Given appropriate weather and current conditions it is possible to camp on separate islands each night. And we usually explore other islands and areas throughout the day. Here are some islands we camp on or explore:

  • Posey Island
  • Stuart Island
  • Jones Island
  • Turn Island
  • San Juan Island

Stuart Island Marine State Park boasts a pleasant diversity of activities. The main camping area is located in Reid Harbor which is a popular summertime boating destination. The protected harbor is a great place for reading a book, looking for river otters or simply strolling on the beach. Tucked within a natural valley, the whole campsite is very comfortable and protected. Before or after dinner, one can explore numerous hikes on the island which include a hike to the Turn Point Lighthouse or Tip Top hill. Observant listeners can often hear owls or nighthawks before drifting off to sleep.

Stuart Island Marine State Park has the following amenities:

  • Picnic and Day-Use Facilities
  • Light station tours on select weekends
  • Mooring buoys
  • Campsites
  • Composting vault toilets
  • Potable Water

Jones Island Marine State Park really is an island cornucopia. The fruits of the island are not just limited to its 4 miles of walking trails, serene overlooks and quiet bays. The island also hosts historic orchards used to grow apples and pears. Deer still enjoy these fruits and can often be seen standing bipedal in an effort to reach higher up the trees. Jones island is a great place to camp for multiple nights on a kayak tour in the San Juan Islands.

Jones Island Marine State Park has the following amenities:

  • Picnic and Day-Use Facilities
  • Mooring buoys
  • Campsites
  • Composting vault toilets
  • Potable Water



We provide the following:

Sea kayaks, all related sea kayaking trip gear, safety equipment, transportation to and from Friday Harbor and the launch beach, instruction and expert guides. While camping, meals provided include breakfast and dinner. Our all inclusive listing price includes spacious tents to ensure you will be well rested for adventure. Sleeping bags and pads can be rented for an additional nominal fee – but feel free to bring your own!

What you need to bring:

Beach clothing, beach foot wear, hat, sunglasses, sunscreen, and lunch. Bring a hat, warm sweater and rain jacket if cool, cloudy, windy or rainy. A detailed packing list of camping related household items will be provided after you book your tour!



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

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.

There are many routes to choose from but there is no “Set Route” because we believe in being flexible to the needs and safety of our customers given a multitude of factors.

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.

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.


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. 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).

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.