It’s pretty darn cool to throw poppers on a mud flat for big stripers while 747s take off and land so close that it’s a little unnerving. So is fishing with the New York City skyline in the background, reflecting gold from the morning sun. It’s all part of the experience when fishing Jamaica Bay, a unique ecosystem consisting of 10,000 acres of estuarine marsh and deepwater bays located right smack in the middle of one of the most populated urban areas on the East Coast. In a setting that feels so far away from nature, the fish still thrive. But how?

Salt marshes like Jamaica Bay are some of the most biologically productive ecosystems in the world. It all begins in the calm, shallow waters of the marsh, where sunlight provides energy for the growth of algae in the water and spartina grass at the rim of the marsh, providing both habitat and food for an abundance of critters. Throughout the year, the decaying marsh grass breaks down into detritus, which serves as sustenance for the bottom of the food chain. As the plants decay and sediment builds up, peat deposits accumulate, forming sodbanks that are washed with nutrient-rich tides and serve as habitat for hundreds of different organisms. Worms, shrimps, snails, crabs and baitfish forage for food among the stems, leaves and roots while seeking shelter from predators at the edges of the marsh.

Jamaica Bay is more than just a salt marsh; it is also an estuary, which is a semi-enclosed coastal body of water with a freshwater source, such as a river or stream, at one end and a connection to the open ocean at the other. Estuaries are therefore subject to both marine influences, such as tides, and riverine influences, such as the influx of fresh water, nutrients and sediment. This mix of conditions provides a variety of biological niches within a small area, and along with the abundance of nutrients, food and protection from predators, creates an ecosystem teeming with the critters and baitfish that attract stripers, blues, and other game fish.

However, Jamaica Bay is not your standard estuary. Because of its proximity to one of the most densely populated cities in the world, “J-Bay” has essentially become an “artificial” estuary.

Before much of the development around Jamaica Bay took place, freshwater traveled into the bay from the woods of Brooklyn and Queens, along winding creeks that had salinity gradients that ran from completely fresh at the headwaters to marine in the bay. These natural freshwater sources no longer exist. The Hudson River was also a historical contributor of fresh water to the bay, but the dredging and channelization of the river has removed much of its influence on the bay.

I assure you, however, that there is still plenty of fresh water dumping into Jamaica Bay. Together, the Jamaica and Rockaway Sewage Treatment centers contribute an astounding 258 million gallons of fresh water per day. Some have even speculated that such an influx of fresh water may have created a spawning area for anadromous fish, like stripers, which migrate into fresh water to spawn. In the spring of 2009, I witnessed a massive school of 3- to 6-inch stripers in some very clear water. Yet, according to New York biologist John Waldman, Author of the definitive book on New York City waterways, Heartbeats in the Muck, such striper spawning theories probably don’t hold any water. Striped bass need large rivers to reproduce, and there are no known instances of bass spawning in anything other than this environment. As for those baby stripers that I saw, Jamaica Bay is known to receive young-of-year striped bass from the Hudson River, as do other western Long Island bays such as Little Neck, Manhasset, and Eastchester. The New York DEC surveys this annually and they are seen every year in varying numbers.

This massive influx of fresh water alone is not what gives Jamaica Bay its unique ecosystem. The huge amount of wastewater that is pumped out into Jamaica Bay is indeed treated and is subject to rigorous standards enforced by the New York State DEC, but it is loaded with nutrients. For better or worse, it is common knowledge that the existence of these sewage treatment plants has caused the water in the back areas to contain an above-average amount of such nutrients.

Talking about sewage treatment plants and good fishing in the same breath just doesn’t seem right. Yet, I have to believe that the massive amount of nutrient-rich water they pump out on a daily basis results in increased productivity of algae and other tiny organisms. And so, it is very likely that this begins an extraordinary food chain, as a number of different baitfish and crustaceans feed on the plankton. Perhaps the most prevalent of these baitfish is the filter-feeding Atlantic menhaden, or bunker, that we see in the spring and fall, which rely heavily on algae blooms for food. It sometimes seems as if you could walk across the bunker schools. Nowhere have I ever seen such concentrations of this baitfish.

The largest concentrations of menhaden I have ever seen came in the late fall or early winter of 2001. That was the same year in which one of the sewage treatment plants had to shut down to fix a valve in October. Some 120 million gallons of raw sewage leaked into the bay. The Bay flushed out pretty quickly, but we had some very large algae blooms as a result. That December, at a time when we usually don’t see any adult menhaden in the Bay, there were thousands!

Such a spill would have been devastating to some estuaries, but the tidal movement is strong enough in Jamaia Bay that dead zones, which can result from over-nitrification of the water, simply do not occur. An example of a water body that is harmed by a surplus of nutrients being washed in is the Chesapeake Bay watershed, where dead zones are a more common occurrence.

There is one more big factor that makes Jamaica Bay unique. It has been channelized and dredged, both for navigation and for landfill for JFK airport, which lies on the northeastern outskirts of the bay. There are 20- and 30-foot-deep channels and 30-, 40- and even 50-foot-deep dredge pits, and all of them are adjacent to mud flats, sodbanks and marshes.

So, Jamaica Bay is essentially a semi-closed, 10,000-acre marsh with the usual productivity associated with such systems, plus an excess of nutrients that attract large amounts of baitfish to feed on the resulting algal blooms, with all the deep water needed to draw in large predators. Such predators are not as easily spooked in Jamaica Bay, thanks to the presence of deep water just a tail stroke away. And believe me when I tell you that large bass and blues come right up into the flats regularly to feast on the abundant baitfish.

Jamaica Bay Through The Seasons

Jamaica Bay’s fishing season starts in April, with grass shrimp as the primary food source for arriving predators. Grass shrimp feed on detritus, algae, and dead plant and animal material, all of which are abundant in the bay. Grass shrimp are year-round residents, but some reproduce in the springtime, and the large spawning concentrations draw in stripers to feed, often before they can be found feeding anywhere else on Long Island.

Also in April, we begin to see Atlantic menhaden. Their arrival coincides with the first real algal blooms of the year. In April, bunker tend to be spread out and are a bit more difficult to find than at other times of year. When you do find them, however, there’s a good chance there will be some hungry bass with them. These stripers are particularly hungry and will aggressively attack plugs, poppers and flies thrown in their direction.

May is the most productive month in the Bay. Warmer water and larger algal blooms attract larger and denser schools of bunker. There are times when the sheer amount of these forage fish is astounding. Massive pods of bunker with their dorsal fins and tails protruding from the water’s surface for as far as the eye can see have become commonplace in Jamaica Bay. Bass will then move in to feed on the large schools of their favorite food, and in May they will also be joined by big bluefish.

In May, large concentrations of grass shrimp can spur on blitzes of school-sized stripers in the shallow mud flats. In addition, there are a good number of silversides (spearing) in the bay in May. These fish feed on zooplankton, copepods, shrimp, worms, and even insects and algae, which makes Jamaica Bay’s unique environment a magnet for spearing. These small, slim baitfish bring in fluke, weakfish and cocktail blues.

In June, spearing move in in large numbers, and small crabs also begin to occupy the flats. This draws huge, sometimes tailing, bluefish in a foot or two of water. This wonderful occurrence can create some very exciting situations where you cast to cruising fish. Big bass can be found in the flats at this time of the year as well, but getting them to eat can be difficult. Fluke fishing in the channels really turns on this time of the year, as their food of choice seems to be spearing.

The creeks that wind though the marshes of Jamaica Bay can be really productive in July; however, the fish are mostly schoolie stripers and cocktail blues. Sodbanks provide habitat for crabs, worms and shrimp that bring these opportunistic feeders into this skinny water. Most of these creeks can only be fished at high tide, but when there’s not much going on elsewhere they can be a lot of fun. I’m always surprised that the kayak fleet doesn’t take more advantage of the creek systems, as it seems to me that a kayak would be the perfect vehicle to fish these areas.

When water really starts to warm toward mid July, because of the excessive nutrients and the resulting algae blooms, the oxygen levels begins to drop. Many baitfish and predators begin to flood out of the bay for this reason. On outgoing tides large schools of bunker and spearing leave the bay, making this prime time to fish the current rip lines that form at the mouth of the bay. The baitfish that get swept over the depth change make easy prey for stripers, blues, fluke and the occasional weakfish.

The baitfish exodus extends into August, and occasionally bonito move into the mouth of the bay to take advantage. Swarming into the mouth of the bay, they rip through schools of fleeing spearing, making for wonderful run-and-gun style fishing. Inside the bay, the fishing slows dramatically. There are always some cocktail blues and some snapper blues feeding, but other than that, it’s pretty quiet. Late August marks the beginning of the false albacore run as they intercept schools of bait leaving Jamaica Bay. Some years, albies move pretty far back into Jamaica Bay to feed on the abundant spearing, with some of the larger ones feeding on snapper bluefish. It can be difficult to elicit strikes from these finicky fish, but just watching them tear across the surface within the confines of the bay is pretty cool.

In September, things start to heat up as water temperatures drop inside the bay again. Young-of-the-year Atlantic menhaden, or peanut bunker, begin to come out of the coves and creeks. These baitfish draw the bigger predators back into the bay. The further we get into September, the more the water temperature drops, the thicker the bait gets, and the better the fishing becomes. Mullet, another filter feeder, are also present in the bay during September. If you can find this bait, you can be sure that bass and bluefish will be on the prowl nearby.

Things continue to get better in October as peanut bunker increase in both size and number. Blitzes can erupt in both deep and shallow areas of Jamaica Bay in the tenth month.
In November, when the air temperature begins to drop below 30 degrees and the wind howls, those peanut bunker begin to leave the bay, and the fishing at the mouth of the Bay in the vicinity of the Marine Parkway Bridge gets redhot.

No matter where you’re fishing, the presence of fish can almost always be directly attributed to the presence of bait. And it’s Jamaica Bay’s unique set of circumstances that ultimately allows a diversity of bait species to exist in such large numbers within the bay’s confines. Large predators move in and take advantage of the food supply during the spring and fall, and that in turn gives anglers the opportunity to experience some excellent fishing in this urban oasis.

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