Fort Flagler to Mystery Bay State Park: Easy Paddling on the Salish Sea

Looking for more to explore near Fort Flagler State Park?
Bike the beautiful Bluff Trail and plan an overnight stay at one of Fort Flagler’s inviting campgrounds.

DIFFICULTY

Easy — Sandwiched between Marrowstone and Indian Islands, the waters of Kilisut Harbor are protected and often calm. In my experience, the pull of the tide was minimal. Even when it’s windy at Fort Flagler, you may find the winds die down as you paddle south to Mystery Bay.

CURRENT INFO

More information about both Fort Flagler Historical State Park and Mystery Bay State Park are available on the Washington State Parks website.

GOOD TO KNOW

• To park at Fort Flagler or Mystery Bay, be sure to bring your Washington State Parks Discover Pass. If you don’t have an annual pass, you can buy one online, at the Fort Flagler State Park entrance station, or from one of the automated machines in the day use areas (but be warned, these machines are not always functional). Day passes are available for $10, and annual passes will soon increase from $30 to $45. Check the Discover Pass website for a list of free days to visit.
• Parking at Fort Flagler is available near the boat launch in the day use area. On my visit during Memorial Day Weekend, I easily found a spot near the launch.
• Mystery Bay State Park also offers parking near the boat launch.
• Wear water shoes or sandals when launching. The launch is covered in sharp barnacles.
• Need to rent a kayak or paddle board? Olympic Tours offers rentals near the boat launch at Fort Flagler Historical State Park in the summer. In 2025, they didn’t open until June.
• Olympic Tours also offers guided kayak tours.
• Restrooms are located near the boat launch at both Fort Flagler and Mystery Bay.
• Pets on leash are allowed at both state parks.
• Bring sunscreen, shade hats, and sunglasses. Even on a cloudy day, the glare on the water can be intense.
• Don’t forget life vests! Every person in your boat needs one.
• Bring water and snacks.
• For a post-paddle treat, head to the Beachcomber Cafe at Fort Flagler. This seasonal cafe offers a small menu of burgers and sandwiches as well as delicious soft serve ice cream. Firewood is sold here, along with a small selection of camping and beach gear.
• Always follow Leave No Trace principles.

HIGHLIGHTS

Kilisut Harbor is a beautiful, protected place to explore the Salish Sea by kayak or paddle board. There’s little boat traffic, so you can relax and enjoy the tree-lined bluffs of Marrowstone Island. Fort Flagler Historical State Park is a gem, with history, biking and hiking trails, and camping. Give yourself time to explore on land as well as by sea. While Mystery Bay State Park may be minuscule, it’s a lovely place to launch your boat or enjoy a picnic with views of the bay.

For more expansive views, you can paddle north of Fort Flagler State Park into Port Townsend Bay. Keep in mind the conditions here may be windier and there is often more boat traffic.

THE KIDS’ TAKE

The protected waters of Kilisut Harbor make this a good easy kayak route for kids and families. Of course, conditions on the water are changeable, so assess the weather and wind before you go. It took me 45 to 60 minutes to paddle from Fort Flagler to Mystery Bay on my own, and for some kids, that may be enough. If you have multiple cars, you can arrange a shuttle to return to your starting point rather than paddle back.

Even if you don’t have the time or inclination to paddle the full three miles between the parks, it’s fun to just get out on the water. Mystery Bay is a good spot to explore, with a dock you can paddle under, plenty of boats to ogle in the harbor, and calm waters.

WHILE YOU’RE HERE

I kayaked to Mystery Bay while camping at Fort Flagler Historical State Park. There are two distinctive campgrounds to choose from, the upper loop in the woods, or the lower loop by the beach. The beach is a big draw, and there are beautiful trails for biking or hiking.

Fort Flagler Historical State Park is a great place to dig into local history. Explore the former military gun batteries and take a peek inside the small museum near the parade grounds. Free guided tours are offered several times a week during the summer season, and we enjoyed both the gun emplacement tour and the historical hospital tour. Check the Washington State Parks event calendar for these and other events.

One of my favorite places for food and drink is Finnriver Farm & Cidery in nearby Chimacum. With a tasty variety of fruit ciders (and some good nonalcoholic options), local food, ice cream, a play yard for the kids, and live music on weekends, it’s the place to relax and unwind on a summer evening. From Finnriver, it’s not much further to Port Townsend, known for its charming Victorian architecture, a good food scene, and Fort Worden Historical State Park.

With more time, be sure to check out Olympic National Park. You can take a day trip from Fort Flagler, or add on a few extra nights at one of the national park’s many excellent campgrounds, such as Fairholme, Sol Duc, or Mora. For inspiration, check out my hiking guide for the Olympic Peninsula or take a tour around stunning Lake Crescent.

“Who wants to kayak with me?” I asked our small group as we headed out to the beach at Fort Flagler. A sudden silence hung in the salty air. No matter; others may prefer a relaxing afternoon on the beach, but that wasn’t going to stop me from heading out on the water.

My friend helped me unload the inflatable double kayak in the parking lot near the boat launch. Fortunately, it’s easy to customize the seating to accommodate one person, and I was soon ready to go. The concrete boat launch was encrusted with a thick layer of barnacles and seaweed, so I kept my sandals on as I maneuvered the kayak into the waters of Kilisut Harbor. With Mystery Bay as my destination, I angled the boat to the south and took my seat.

Although there was a cool breeze when I departed Fort Flagler, it quickly died down as I paddled southward. To my left, charming cottages and luxurious island retreats gazed placidly across Kilisut Harbor from the bluffs of Marrowstone Island. Across the harbor on Indian Island, there were no such signs of human habitation. Indian Island houses an active naval magazine and no trespassing is allowed, so I recommend sticking near Marrowstone Island while you paddle.

About 45 minutes into the trip, I paddled into Mystery Bay. A low, rocky point marks the entrance at the north end of the bay, and the water here is quite shallow. Keep an eye on the depth as you go.

On my trip southward, I saw only a few other boats out on the water. Despite the fact that it was Memorial Day Weekend, Kilisut Harbor was quiet. This may be due to the fact that the harbor is essentially a dead end. At the far south end of Marrowstone and Indian Islands, only a small, unnavigable channel separates them, forcing any boaters to turn back.

There were quite a few sailboats moored in Mystery Bay, however. Perhaps their owners were spending a leisurely weekend in the bay, or perhaps they had homes elsewhere on Marrowstone Island. I paddled past them as I skirted the north shore of the bay and headed for Mystery Bay State Park.

Mystery Bay State Park is a tiny treasure on the north side of the bay. Here, what you see is what you get: a boat launch, picnic area, restroom, small pebbly beach, and a long dock extending into the bay. Although I didn’t have time to disembark and explore on foot, I couldn’t resist paddling under the dock before turning around.

After a good look at Mystery Bay, I began the return trip north on Kilisut Harbor. More clouds began to streak the sky as I paddled, but the water remained calm with only a light breeze ruffling the surface.

When out and about of the Salish Sea, there’s always the chance you may spot some wildlife. I can’t deny I was hoping for a sighting on my journey, so I was delighted to see a small dark shape pop up from the water when I turned to look behind. Was that what I thought it was? Yes, I confirmed after turning to look once more. The head of a harbor seal appeared again, this time a little closer.

I didn’t turn the boat around, but continued to watch, hoping for another glimpse. Sure enough, there it was, and this time there were two. Both seals drew nearer, but were still a good hundred feet away. They disappeared and resurfaced yet again, giving me one last look before sinking back down into the water.

It was a beautiful end to the trip. On shore at Fort Flagler, my friends helped bring in the kayak. Everyone else had already returned to the campsite, where a delicious camp dinner awaited. It’s not often I have to chance to paddle on my own, but after a delightful trip from Fort Flagler to Mystery Bay, I can’t wait to do it again.