Explore Great South Bay's Year-Round Fishing Opportunities

Pictured above: Big stripers will move into Great South Bay after schools of adult bunker.

The largest bay on Long Island holds 12 months of gamefish opportunities.

The South Shore of Long Island is defined by its bays. Together with the barrier islands that give them shape and the inlets that bring them life, they form what geologists call a “barrier system.”Anglers just call them good places to fish.

That’s because the bays are very productive. Mud-bottomed shallows, bordered by sod banks, provide vital nursery areas for baitfish and gamefish alike, and hunting grounds for larger predators. In the midst of the bay, tide-scoured channels slice through the shallows, providing a host of fish species plenty of places to ambush the crabs, shrimp and baitfish that are washed through the cuts on each flowing tide.

Great South Bay, as its name suggests, is the largest of all the South Shore bays. Its western border, imprecisely defined by a string of marsh islands, is somewhere near Amityville. To the east, things are more certain, as Smith Point slices down to form “The Narrows,” which leads to Moriches Bay.

That makes Great South Bay about 26 miles long and, for most of that length, roughly 3 miles wide. It has an average depth of a little over 4 feet, but like any barrier lagoon—which, technically, is what the South Shore bays are—its depth varies widely. There are a few spots more than 30 feet deep, and plenty of flats where a gull can wade while keeping its belly perfectly dry. Those flats can surprise fishermen used to deep water.

I first ventured out onto Great South Bay over 30 years ago, on a boat without a LORAN (GPS was still years in the future). A heavy fog had settled in, and as I followed my compass down the Babylon Cut, I passed a number of boats anchored up along the cut’s edges, waiting for the murk to clear. As I passed, a number of them pulled up their anchors and followed, like children behind the Pied Piper—and the results were somewhat the same.

At some point, I wandered out of the channel and felt my outboard touch bottom. I immediately cut power. The boats behind me did the same, and re-anchored, while I grabbed an 8-foot oar off the deck and started poling toward what I hoped was deep water. The other boats, all apparently without a push-pole or oars, remained behind, although their curses followed me quite a way through that fog-thickened air…

Despite its troublesome flats, Great South Bay still holds about 8.7 billion cubic feet of water, and that much water can hold an amazing variety of fish.

At one time, abundant white perch and herring provided action all winter. The perch were caught on the fringe of the bay, in the myriad tidal creeks that feed in from the north. The herring, on the other hand, usually stuck closer to the inlets, with most being caught from the State Channel piers at Captree State Park.

For the past few years, both white perch and herring have been hard to come by, although anglers who work hard enough can still catch a few. However, for most people, Great South Bay’s fishing season begins on April 1 with the start of the winter flounder season.

Unfortunately, the flounder, too, have grown pretty scarce. At one time, fishermen brought them home by the bucket; today, a “limit catch” means two 12-inch fish, and there are a lot fewer boats on the early spring bay.

Even so, a few anglers get out every opening day. They seek their two fish on the Hecksher Flats or in the shallows south of Good Samaritan Hospital, the Babylon Pool or the Bergen Point Sewer Plant, where a dark bottom traps the heat from the sun and radiates it back into the water above. The party boat fleet at Captree also gets in on the action. A few boats go out on opening day, while the rest wait for the weather, and the fishing, to improve later in the month, when the flounder bunch up as they move toward the inlet.
At that point, spots such as West Channel, Dickerson Channel and the bay off the Fire Island Lighthouse begin to get crowded as party boats and private vessels converge over whatever fish might be around.

Just a week or two later, about the first week in May, Great South Bay comes alive as a host of species appear on the scene.

Striped bass anglers might consider it heresy, but of all the fish in the bay, weakfish are, by far, my favorite. I’m not sure why. Folks to our south call them “sea trout,” and maybe part of the attraction is that, like their freshwater namesakes, they’re just beautiful fish. Their bright silver sides shimmer with lavender highlights, and are framed by deep yellow fins that seem to glow in the light of a new-risen sun. Weakfish seem both delicate and deadly, their sharp upper fang contrasting with their sleek, supple form.

Big females enter the bay in mid-April, where they lie in the deep channels and fall victim to gill nets until waters warm. By the first week of May, they’re generally moving, and will take lures fished very slowly right down on the bottom. Even down deep, the fish are easily spooked, so angling is best during times when light levels are low and few boats are moving.

At night, once the bay quiets, weakfish often move up onto the flats to hunt crabs and grass shrimp. They’ll also set up, like trout, in feeding lanes, slurping down shrimp and small baitfish in places where the current breaks around piers and other hard structures. However, the biggest weakfish of all are usually found in deep channels, where they are caught by anglers who drift whole sandworms, and sometimes live bunker, by the light of the moon and stars.

Nearly a decade ago, the weakfish population hit record low levels; since then, one decent year class has allowed the stock to rebound just a bit. Still, weakfish can be a challenge to find. Even so, anglers trying for them seldom have time to be bored.

Mostly, that’s thanks to the bluefish, which flood through the bay in the spring. Sometimes the bluefish stay deep, and you’ll only learn they’re around when one chops off a bucktail. More often, especially at dawn, they’ll shatter the surface in pursuit of their prey. I’ve seen so many schools of small blues chasing bait between Point O’ Woods and Ocean Beach that there weren’t enough birds in the air to dive on them all at the same time.

Down deep, where no one can see, other fish are feeding. Fluke, like weakfish, move into the bay during April. And, like weakfish, they’ll take bucktails and soft plastics fished close to the bottom, although most serious fluke fishermen drift tried-and-true baits such as spearing and squid.

Big porgies and black sea bass also swim in May waters. We’ve caught a few while casting for weakfish, although anglers using bait and chum catch quite a few more. Now that fisheries managers have fully restored the scup population, the porgy season usually begins on May 1; however, black sea bass season normally begins quite a bit later, so fish caught in May cannot be retained.

And then, of course, there are stripers.

School fish show up early in May. They’ll take plugs and bucktails cast along the edges of the State Channel, and are suckers for clam bellies drifted around bridge pilings, sod banks and structure such as the Kismet Reef. Bigger fish move in a little later. Most of them stick near the inlets, but others go deep in the bay, where they hunt menhaden and other small baitfish through the night, so long as the water stays cool.

Unfortunately, bad things can happen as the bay’s waters warm. Around the middle of June, algae blooms, fed by nitrogen runoff from heavy spring rains, often spread through the bay. When that happens, the bay becomes turbid and oxygen levels drop.

The worst of the blooms, the so-called “brown tide,” fills the water with tiny single-celled plants that smother the clam beds and turn the water into a sludge-colored soup that foams darkly away from a moving boat’s bow. It can turn off fishing for much of the summer.

Historically, a combination of summer algae blooms and high water temperatures turned the eastern end of the bay into a sort of “dead sea.” However, since Superstorm Sandy cut through Fire Island and allowed fresh ocean water to pour into the eastern bay, those historical conditions have been completely reversed. Thanks to “New Inlet,” the bay was reborn.
That’s what makes Great South Bay, like all barrier systems, a very special place. It is constantly changing, and no two years are ever the same. Summer’s tropical systems and winter’s nor’easters change the shape of the bottom and the islands, at will. And when changes like the New Inlet bring cool, clear water in from the sea, old summer patterns return to the bay.

Striped bass become scarce in the summer, although a few fish still swim close to deep water and feed in the dark of the night. There’s surface action with bluefish, but only at dawn when the water is coolest. I found plenty of blues south of Hecksher last summer, but they were always done feeding by 7 a.m.

Some fluke will also stay “inside” during the summer, although most abandon their spring hunting grounds deep in the bay and move closer to the inlets, where they take advantage of the cooler water brought by each incoming tide.

Weakfish, too, leave their usual spring haunts. A lot of the bigger ones move into the inlets and ocean, though, a few will venture into the creeks seeking cinder worms and bunker. The best cinder worm bite I’ve ever seen on Long Island occurred in a creek up in Copiague. A friend who owned a marina there tipped me off when he saw some big weaks swimming through the beams of his dockside lights.

The most reliable summer weakfishing is for the smaller fish that often school on the flats off Sayville, Blue Point and Hecksher State Park. Many are below the legal size limit, but there can be bigger fish in the mix.

Yet, when we talk about fishing the summer bay, it’s often the small fish that matter.

Summer means time off from work and kids off from school. There are few better ways to spend time with children than bottom fishing in Great South Bay. The fish won’t be huge, but they come in all shapes and colors, and anyone who anchors north of the channel off West Fire Island or drifts the long stretch of deep water around Ocean Beach will find more than enough fish to keep young hands busy.

“Sand” porgies and “pin” sea bass dominate the action. Most will be too small to keep, but the sheer numbers will be so high that a few legal fish will eventually find their way into the cooler; over the years, I’ve put kids into sea bass as big as 2 pounds. Northern kingfish can also be pretty common, and from the beginning of August onward, snapper blues become an ever bigger part of the mix.

In recent years, Great South Bay has enjoyed a resurgence of blowfish, which put on a show guaranteed to get young anglers laughing, while the occasional triggerfish will give them a chance to see something new. But, never believe that such small creatures are the only fish that enter the summer bay.
Sand tiger sharks, some more than 7 feet long and weighing well over 100 pounds, quietly come into Great South Bay. They keep a low profile and few are caught by anglers. Nevertheless, they are there.

A few years ago, a team of biologists asked me to help them plant acoustic tags in some sand tigers. The first step was catching a few of the sharks inside Great South Bay, something that I had never done.

It took me a while to figure out when and where the fish could be caught. Eventually, we ended up within the bulkhead of a Fire Island marina, where bait such as bunker bunched up and created a living chum line. I felt a little funny tied up to some pilings, with baits in the water and reels shining gold in the sun, while folks 20 feet away sipped fruity drinks in their boats’ cockpits and kids in bare feet padded around on the boards of the dock.

But, as I said, the sharks were there. We had two solid hookups in maybe four hours, one with a big fish, the other with a small one. And we would have found more if violent thunderstorms hadn’t roared in from the west.

That was the climax of one year’s bay season. As fall arrives and the water cools, the sand tiger sharks, along with a lot of the other fish in the bay, begin to move seaward. By mid-October, fishing is usually limited to striped bass, bluefish and one new arrival, the blackfish.

Blackfish live close to hard structure, so they can be tough to find in the sand-bottomed bay. Bridge pilings can provide some good fishing, as can the boats, barges and rubble that make up the Kismet and Yellow Bar reefs. Blackfish will hang around any sort of junk on the bottom, so anglers who find the remains of old sunken boats or other debris often manage to catch some nice fish from these small bits of structure.

Still, it’s the striped bass that dominates fall fishing efforts. Menhaden and other baitfish stage in the lower bay before beginning their migration to warmer waters. The bass concentrate in response, and anglers, in turn, will follow the stripers. Most of the fishing takes place between West Channel and Fire Island Inlet, where boats live-line menhaden during the day and drift eels in the depths of the night.

A smaller number of anglers fish in the State Channel, casting plugs around cuts and drains in the sod banks or fishing menhaden chunks on the bottom. Others troll shad bars near the steep channel edges, and catch quite a few decent fish while avoiding the crowds.

But, slowly, the stripers and bluefish move down toward the inlets and, in time, they are gone.

Bluefish usually leave first, in early November, and by the time Thanksgiving rolls around, most of the striped bass have moved on too.
Then, a few herring slip through the channels, and a few lingering stripers encounter them there.

But for most of the fish, and almost all of the anglers, the season is over. Great South Bay abides, quiet, until spring rolls around.