Port of the Islands & Faka Union Bay: The Eastern Gateway to the Ten Thousand Islands

What Is Port of the Islands?

Port of the Islands is a small resort-and-marina community that sits right on the Tamiami Trail (U.S. 41), roughly halfway between Naples and Everglades City. It’s easy to miss if you’re not looking for it — a cluster of condos, a hotel and a working marina tucked into the mangroves where the highway crosses the Faka Union Canal. For boaters, though, it’s a landmark: the marina’s boat ramp and docks give private vessels a straight shot down the canal to Faka Union Bay and out into the Ten Thousand Islands backcountry, without ever touching Marco Island or Goodland. Anglers running the interior creeks, paddlers doing multi-day trips through the refuge, and guests staying at the resort all use it as a launch point. It also borders two protected tracts — Fakahatchee Strand Preserve State Park to the north and Picayune Strand State Forest to the east — so the whole area feels more like a wilderness outpost than a marina district, with swamp buggy and airboat operators dotted along the same stretch of the Tamiami Trail running trips into the strand and the glades to the north.

The Faka Union Canal’s History

The canal Port of the Islands sits on wasn’t always meant to move boats. Faka Union Canal was cut in the 1960s and ’70s as part of a huge land-development scheme that tried to drain the swamp south of Golden Gate Estates into buildable house lots — the same era that platted thousands of Southwest Florida lots that never saw a house. The canal, along with two others nearby, worked too well: it drained water off the land far faster than the natural sheet flow that used to feed the Ten Thousand Islands estuary, drying out cypress strand and dumping fresh water into the bays in unnatural pulses. Most of those platted lots were never built on, and in the decades since, state and federal agencies have worked to undo the damage, plugging sections of canal and pulling out old subdivision roads to push the water back toward its historic path. Faka Union Canal is now as much a restoration case study as it is a boating route — you’re running through an Everglades repair project every time you idle down it.

Winter Manatees at the Marina

Port of the Islands’ other claim to fame is manatees. When Gulf water temperatures drop below about 68°F, typically from November into March, manatees can’t tolerate the cold for long and go looking for warmer refuge. The canal basin at Port of the Islands tends to hold heat better than the open bay, so on cold mornings you’ll often find a handful of manatees loafing near the marina, surfacing to breathe in the calmer, warmer water. It’s not the concentrated, hundreds-strong herd you’d see at a Crystal River spring — expect small, scattered groups rather than a crowd — but it’s a genuine, reliable pattern that draws visitors and photographers every winter. The same cold-front behavior plays out quietly around Rookery Bay and other sheltered basins near Marco Island, which is where our captains most often spot manatees on the water. Manatees are protected under both state and federal law, so if you do spot one, admire it from a distance and let it surface and move on its own. Check our wildlife guide for what else surfaces alongside them.

Faka Union Bay & the Wildlife Refuge

South of the marina, the canal widens out and empties into Faka Union Bay, a shallow, mangrove-fringed bay that marks the eastern edge of the Ten Thousand Islands National Wildlife Refuge. From there, the water opens into one of the last true wilderness estuaries left in the Lower 48 — hundreds of mangrove islands, oyster bars and tidal creeks with no roads, no docks and no cell service once you’re a few miles in. Boaters launching from Port of the Islands can run south toward Everglades City and Chokoloskee, or work the bay itself for snook, redfish and the wading birds that stack up on the flats at low tide. Bottlenose dolphins work these same flats year-round, and it’s not unusual to spot roseate spoonbills, ospreys or a bald eagle working the mangrove edges as the tide turns. It’s wild, tide-dependent water that rewards local knowledge and punishes guesswork — the channels shift, the flats go dry fast, and there’s little margin for error if you don’t know the bay. Our Ten Thousand Islands guide covers the wider refuge if you want the full picture of what’s out there.

Port of the Islands vs. Goodland

Port of the Islands and Goodland are really two doors into the same wilderness, and it helps to know which one gets you where. Port of the Islands is the eastern gateway, off the Tamiami Trail, closest to Everglades City and the refuge’s southern reaches. Goodland is the northern gateway, tucked behind Marco Island, and it’s where our boats actually dock. Neither one is the better option — they just open onto different sides of the same roadless water.

If you’re staying at Port of the Islands or just passing through on the Tamiami Trail, the marina and canal are worth a look, but there’s no public tour desk there and it isn’t a Sand Dollar departure point — our boats run out of Marco Island, Goodland and Naples, on the opposite side of the same refuge. The upside is you don’t lose anything by booking from our side: the mangrove islands, sandbars and wildlife you’d see pushing south from Faka Union Bay are the same water our captains run every day from Goodland, just approached from the north instead of the east. If manatees, dolphins and untouched barrier islands are what drew you to this stretch of coast, our dolphin tour covers that same wild backcountry with a captain who can actually explain what you’re looking at. Browse the rest of our destinations guide to see how the pieces of the Ten Thousand Islands fit together.