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Kayaking Marathon: Boot Key has beautiful mangrove tunnels, lagoons

Boot Key is an undeveloped island disconnected from the bustling city of Marathon by a bridge that closed 15 years ago. Once slated for development, Boot Key has remnants of a few original roads and a building or two accessible only by water.

Mostly, Boot Key is a pristine mangrove swamp, one you can explore on unmarked kayak trails that take you over clear water through narrow mangrove tunnels. Kayaking Marathon and Boot Key is an easy and beautiful outing.

Kayaking Marathon: A mangrove tunnel on the Boot Key kayak trail. (Photo: Bonnie Gross)
Kayaking Marathon: A mangrove tunnel on the Boot Key kayak trail. (Photo: Bonnie Gross)

While it is sometimes a challenge to follow the trails, we were able to easily find our way for a delightful quiet paddle. On a windy day, this protected route was a perfect place to paddle.

Launch site for kayaking Marathon and Boot Key kayak trail

You launch from a sandy area on Sister Creek, at Sombrero Beach, where Sombrero Beach Boulevard ends.

This launch site offers two challenges:

On afternoons of good beach days, all the free parking spaces may be filled. Best bet: Go earlier in the morning.

Secondly, it at first appears the launch is fenced off. But there is a pedestrian gate in that fence through which you can enter and carry your kayak.  If you have a cart, it will come in handy – it’s about 100 feet to the water.

The launch site is sandy and adjacent to the fishing pier. It is surrounded by rocks large and small that you have to avoid. 

Boot Key kayak trail map from Florida Paddling Trail Association.  The route described in this account makes a loop by connecting the trail across the lagoon at the center.
Boot Key kayak trail map from Florida Paddling Trail Association. The route described in this account makes a loop by connecting the trail across the lagoon at the center.

The Boot Key kayak trail: An adventure to find and follow

From the launch site, you paddle away from the ocean along a wide waterway popular with power boaters, so stick to the shorelines. You paddle 15 or 20 minutes with mansions on your right and undeveloped Boot Key on your left.

Kayaking Marathon and Boot Key: The put-in site on Sister Creek adjacent to Sombrero Beach. (Photo: Bonnie Gross)
Kayaking Marathon and Boot Key: The put-in site on Sister Creek adjacent to Sombrero Beach. (Photo: Bonnie Gross)
Kayaking Marathon and Boot Key: Carry your kayak through this opening in the gate and down to the sandy put in site. (Photo: Bonnie Gross)
Kayaking Marathon and Boot Key: Carry your kayak through this opening in the gate and down to the sandy put in site. (Photo: Bonnie Gross)

Keep to your left on this waterway, passing an area where many sail boats are moored and a couple have sunk. (After Hurricane Irma in 2017 a few hundred boats sunk here. Those were removed; so these have gone down since then.)

If you take the left turn into the interior of Boot Key you’ll eventually reach a point where you must choose to go right or left into two wider lagoon areas. There is a trail through the mangroves that takes you on a loop that connects the two. If you take this loop, you’ll have about a two hour paddle from launch to take-out.

For a longer trip, as you see on the trail map above, you can paddle out of Boot Key through the lagoon on the right and circumnavigate the island.

There are no signs indicating where the trail exits these lagoons. You’ll see openings in the mangroves and you have to watch for ones that look like they’ll go through. (We watched for cuts on branches indicating somebody had groomed the trail.)

Satellite maps on our phones also helped guide us.  

Kayaking Marathon: A sunken boat along the Boot Key kayak trail. (Photo: Bonnie Gross)
Kayaking Marathon: A sunken boat along the Boot Key kayak trail. (Photo: Bonnie Gross)

We enjoyed the adventure of finding and following the trail. A few strategies that worked for us: We were always ready to retrace our steps if we sensed we’d gone down the wrong waterway. We knew a kayak outfitter was taking a group through this trail system in the opposite direction, so when we got caught in spider webs, we knew we’d taken a wrong turn – the other group should have cleared the spider webs.

If you’re nervous about finding your way back, consider a piece of string to mark the entrance to an opening that you may need to find again if you need to backtrack.

We also watched the direction of the tidal flow to make sure we were on our desired route.

Along the way, we enjoyed the beautiful mangrove forest with clear shallow water and periodic openings into wider lagoons where we admired upside down jellyfish and an occasional wading bird. Sometimes the tunnels were so narrow we pulled ourselves forward gripping mangrove branches.

The shallow lagoons are best paddled at medium to high tide.

We’d love to return on a less windy day so that we can find our way out into Boot Key Harbor, hug the island’s shore and perhaps have lunch at the Chiki Tiki Bar and Grill at Burdine’s Waterfront, which overlooks Boot Key and is included in our guide to Keys tiki bars.  

Sombrero Beach fishing pier, adjacent to the launch for kayaking Marathon and Boot Key. (Photo: Bonnie Gross)
Sombrero Beach fishing pier, adjacent to the launch for kayaking Marathon and Boot Key. (Photo: Bonnie Gross)

Outfitters for kayaking Marathon and Boot Key

Don’t have a kayak? There are several outfitters serving the area who run tours and deliver rentals here. Check out:

Caribbean Kayaking Tours

Keys Kayaking LLC

Florida Keys Kayak & Paddleboard

Florida Rambler information for visiting Marathon

Our guide to things to do in Marathon.

Tour the Turtle Hospital in Marathon

Old Seven Mile Bridge: fabulous place to stroll, bike and gaze

Visit Pigeon Key, historic island in the middle of Old Seven Mile Bridge

Best Florida Keys tiki bars, including three in Marathon

Curry Hammock State Park: Great kayak trail and camping


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