San Juan Kayak Tours

We offer a wide range of San Juan kayak tours based in the town of Friday Harbor Washington. All kayak tours have a shared focus on wildlife education, whale watching, and adventure. San Juan Island offers the best whale watching opportunities near Seattle Washington.

San Juan Island offers a great blend of accessibility, wildlife diversity, and natural beauty. Pacific Northwest kayaking is defined by rocky shorelines, swift currents, wildlife and amazing sunsets. The opportunity to kayak with killer whales on San Juan Island is an awesome experience. We select a location to paddle that maximize our potential for killer whale encounters.

We hope you choose Discovery for your San Juan Islands kayak tours.

San Juan Kayak Tours


The Full Day Kayak Tour spends the most time on the west side of San Juan Island in prime whale watching territory. The travels along the coast to the Lime Kiln State Parks to a small pocket beach for lunch and a short hike to the lighthouse. We currently have one daily departure with groups of no more than 8 guests. This is the perfect option for those looking to spend the most time on the water while visiting San Juan Island.

Daily Departure 11 AM


The Half Day Kayak Tour is extremely popular. The kayak routes travel through the best whale watching region of San Juan Island. The time on the water is perfect for guests looking to pack in multiple activities in one day. With 3 daily departures, the half day kayak tour easily fits into your travel schedule.

San Juan Islands Kayak Tours

Tour Highlights

  • 3 Daily Departures (8 AM, 1130 AM, 130 PM)
  • Best Whale Watching Routes.
  • Professional Sea Kayak and Naturalist Guides
  • Best Value on San Juan
  • Quality Equipment
  • Small Groups


Sunsets on San Juan Island are simply stunning.Kayakers at sunset on San Juan Island.

Departing from the west side of San Juan Island is the best location to enjoy the sunset. We are on the water for sunset, so be prepared to be out late and back in town after dark. Orca encounters during sunset is a huge bonus. With little boat traffic, we can enjoy them all to ourselves. 

Tour Highlights

  • Sunsets are simply amazing.
  • Whale Watching Kayak Route
  • Professional Guides
  • Small Groups

Bioluminescence Kayak Tour

Most unique kayak tour offerings on San Juan Island. Over the years the “Bio” Tour has grown in popularity that it is recommended to reserve available slots months in advance. We limit the departures to only certain months and only Kayaker paddles through bioluminescence. certain times of the month to miss days during the full moon. There is only one departure per evening with a small group of guests. If you have not experienced kayaking in bioluminescence, this is a must do to add to your San Juan Island vacation.

Tour Highlights

  • Most Unique Kayak Tour on San Juan Island
  • Professional Sea Kayak Guides
  • The most experienced company leading tours at night.

3 Day Kayak and Camping Tour

We offer several multi-day kayak tour options but the 3 Day Kayak Tour has always been the favorite choice for travelers. Three days offers the perfect amount of time to travel the islands and enjoy the camping experience while searching for whales. Our 3 Day Kayak Tours is the most inclusive tour on San Juan. All the kayak and camping equipment is Killer whales passing by the front of kayakers on San Juan Island. provided. All meals (Breakfast, Lunch, and Dinner) are provided. We take care of all the details so you have little to worry about while traveling. Traveling in the smallest groups allows us to select some of the best camping areas larger groups simply will not fit. Our guides have the most experience kayaking the islands and provide you with the best options for camping and kayak routes. This is a perfect option for the adventurer who is looking for a memorable kayaking experience on San Juan Island.

Tour Highlights

  • Smallest Group Size on the island.
  • Best Value for your money
  • All Equipment and Food provided
  • Experienced Expedition Kayak Guides


When you read about whale watching Seattle Washington this really means from San Juan Island. Whale watching is one of the main attractions on San Juan Island. Visitors can choose to visit the Lime Kiln State Park and chance an encounter from shore, purchase tickets for a whale watch cruise departing from downtown Friday Harbor or reserve a kayak tour and head to the west side of San Juan Island for a day on the water.

Many visitors to the island are not aware that the Southern Resident Killer Whales are listed on the Endangered Species List and have been since 2005. There are many laws and guidelines that govern how we behave around the animals.

We follow strict best practices guidelines around all animals and as a member of the San Juan Island Kayak Association, we strive to set the best example while on the water.

The following are the best practices in the presence of killer whales:Whale Watching Guidelines Poster.

  1. Maintain a distance of 200 yards from the side of the animals. To adhere to this guideline we follow a specific set of procedures to minimize our impact on the whales. If whales are in the area we will paddle near shore and observe their travel behavior. If the animals approach to within 200 yards of the shore we will stop paddling and raft our kayaks side by side in an appropriate area. At this point, whales may approach and pass extremely close to our kayaks. Our goal at this point is to stay put and let the animals clear the area.
  2. If we are paddling off shore and notice the whales approaching directly in front of us (the travel path). We will move inshore before we are within a 400-yard distance from the animals. We want to maneuver to avoid being in the travel path of the whales. This can be tricky at times so pay attention to your guides, as they are experienced in working around the whales.
  3. If we are on the shore preparing to launch or having lunch, we will not leave the shore if the whales are traveling near shore. We can easily have a great experience viewing them from the beach.

This is a short list of protocols we follow to minimize our disturbance to the whales.  It is important to note that all vessels whether under motor, wind or human power have to abide by the 200 yard and 400-yard rules.

The whales passing whale watchers.For a detailed list of guidelines, laws, and fines please visit the Be Whale Wise website.

In many ways, kayaking can be one of the best ways to experience killer whales. All guides are trained naturalists and have extensive knowledge about killer whales. By traveling by kayak in small groups we are able to be in better positions than larger groups to see the whales when they make a pass. Kayaks are a minimal impact way enjoy the marine environment; sitting close to the water provides an unparalleled experience around the whales.

Discovery Sea Kayaks is a member of the San Juan Island Kayak Association (SJIKA). The association works hand in hand with NOAA and The Whale Museum to develop the best practice guidelines for commercial kayak tour operators on San Juan Island. We hold ourselves to the highest operating standards to provide the best kayak tour with minimal impacts or disturbances to wildlife.

Southern Resident Killer Whales are under survival pressure and we ask all visitors to respect the laws and guidelines in place to help protect them.

San Juan Island Kayak Association LogoThe Whale Museum LogoBe Whale Wise Logo