Thompson and other flats anglers often take the nearby Lakes Passage to the west for protected and less-crowded grounds. The Lakes Passage is a shallow, protected cove averaging four feet deep that separates the Gulf and the Atlantic on the harbor’s west side, by the Northwest Channel. Its waters often remain clear even when water everywhere else has turned muddy, but entrance to the passage is tricky. Near the mouth of the harbor, between high flats that often strand unwary boaters, a couple of stakes, barely visible, mark a series of quick S turns into the Lakes. Boaters should consult charts before trying the entrance.

Captain Phil Thompson with a harbor tarpon, about to be released.

On rough winter days, the harbor is the place to be for flats skiffs and light-tackle boats. The sure thing is to anchor in the Northwest Channel, start chumming and bottom-bouncing 3⁄ 4-ounce jigs tipped with cutbait or shrimp. Resident muttons, other snappers, seasonal cobia, yellow jacks and mackerel keep the rods bent. Live shrimp are also readily available from local marinas in the winter and make surefire baits either freelined or bottom-fished with splitshot or a slip-sinker. Other good and protected spots for anchoring in the harbor include Sailboat Basin, right up against Key West, and Calda Channel. Those spots always offer a quick fix of fishing, no matter the weather, and with live bait, there’s no telling what you’ll catch.

Captain Joe Green has fished a light-tackle boat all over the harbor, and everywhere else around Key West, since 1978. He laments the decline of the harbor fishery over the last couple of decades and attributes the change to the commercial and residential development ongoing in the Lower Keys. He cites the case of Tank Key, in the harbor a few hundred yards north of Key West. In the ’90s, before Tank Key was developed into the luxury resort property known as Sunset Key, “we constantly caught fish right in front of it,” Green says. “We could count on schools of tarpon there in the season, and numerous cobia every day through the cold months. Now, the fish have moved out due to all the traffic.”

“Decades ago,” says Green, “we’d only go into the harbor on those windy days. We found the cobia and permit coming into the harbor in the winter, and the tarpon plentiful in the spring, and now a lot of guys fish the harbor as a first option.

“I’ll go there on windy days and to get pinfish for cobia bait, and for blue runners for offshore baits,” Green says, and it’s an important point.

The harbor and its markers yield all manner of baits. Blue runners, pilchards, ballyhoo, mojarra and other species all flourish in the harbor and its seagrass environs, which attests to its value as a nursery, shelter and foraging ground for the entire surrounding fishery.

“But the real season typically starts in February,” Green continues, “when you can target tarpon, permit and cobia, good snapper and blacktip shark action around Pearl Basin, just north of the harbor.”

In April and May, he adds, the fish move and filter into the Fleming Key area and to the tip of Key West, near the mouth of the harbor, on their annual migration pattern. Then you have to search around for them in Jack Channel, around Sunset Key and Calda Channel, until you find them.

“I really enjoy fishing Pearl Basin in those cold months,” Green says. “That’s the best time of the year because there’s little boat traffic, no jetskis, and no parasails. You can find a school of permit and have a great day, release fishing, of course. I’ve had days recently catching up to 30 permit, plus tarpon, snappers and cobia.”

Year-round, the many patch reefs throughout the harbor area teem with snappers and groupers that give kids the fight of their lives. Patch reefs also host schools of visiting Spanish mackerel in the winter and the occasional cobia. Florida Sportsman Fishing Chart No. 011 marks numerous wrecks and patch reefs within minutes of local marinas, which makes the harbor a great destination for family fishing with a minimum of fuss.

Key West Harbor remains a vital and healthy link to the area’s varied fishery. With a measure of care and foresight from all those involved, the harbor should sustain itself and continue to surprise all of us who call it home, for however briefly, with its abundant marine life.

FS