Fall Run across the Mid-Atlantic

As the days shorten, beaches empty, and vicious greenhead flies finally disappear, the Fall Run across Mid-Atlantic states begins. Known as a period of change from September to December, the Fall Run presents some of the best and unique back bay fishing opportunities of the year if you are willing to put in the time to gain an understanding of the dynamics of your local estuary or bay.

Fish migration out of back bays is driven by change, as species move in response to shifting environmental conditions (water temperature, day length, etc.). This movement is primarily triggered by the search for overwintering habitat, forage opportunities, or spawning needs. For example, adult summer flounder depart back bays during the Fall Run to spawn on the outer continental shelf. By understanding the basic movement dynamics of the target species and their associated habitat choice during the late season, an angler can position himself to intercept a mixed bag of species on a late September outing in a kayak.

Although many kayak anglers associate the Fall Run primarily with massive schools of trophy-sized striped bass, another striped species that has recently received increased attention is sheepshead. Historical records indicate sheepshead were once widespread in the northern Mid-Atlantic region (Lower New York Harbor, Raritan Bay, Jamaica Bay) prior to the 1900s. However, the subsequent rapid decline of populations in the mid-20th century is not well understood. Fortunately, sheepshead have made a resurgence in Mid-Atlantic bays and estuaries in the past two decades. So, does the re-appearance of sheepshead in Mid-Atlantic represent an expanding range of southern populations, or the re-colonization of historical habitat as a new founder population that is here to stay?

Chase Wunder (Ph.D. Student at Rutgers University), Dr. Thomas “Motz” Grothues (Director of Rutgers University Marine Field Station), Dr. Keith Dunton (Associate Research Professor at Monmouth University), and volunteer anglers with the Rutgers Fish Tagging Research and Education Program (FiTREP) are actively trying to answer these questions by tagging sheepshead with electronic acoustic transmitters (tags) throughout the Mid-Atlantic region. In 2025 the team tagged a total of 30 Sheepshead from pedal driven kayaks and ramped up the efforts in 2026 with plans to tag a total of 100 fish from inshore New York to Delaware.

South of the Mid-Atlantic, sheepshead are known to begin leaving inshore structure in the fall to spawn around nearshore wrecks and reefs from late February to April, however the specific timing can vary based upon coastal water temperatures and latitude. Post spawn sheepshead begin to migrate back inshore, ready to feed on the buffet of mussels, clams and crabs available in estuarine environments. While these movements are well documented south of Cape Hatteras, little is known about the dynamics of sheepshead behavior in the Mid-Atlantic.

Tracking data from the summer through late fall of 2025 showed acoustically tagged sheepshead utilizing a wide variety of habitats within a southern New Jersey estuary including tidal creeks, salt marsh embankments, aquaculture lease areas, and hard structure surrounding the inlet. Many tagged sheepshead tended to remain close to the same locations they were tagged for extended periods of time, with some fish being detected at the same location from July through October. Sheepshead began migrating offshore between August and October, with 60% of tagged fish moving offshore in October towards the 3-mile line. Interestingly, a few stragglers were detected in November.

The acoustic tags have approximately 2.5 years of battery life, which will allow the team to track offshore and inshore movements in 2026 and determine if sheepshead are spawning and restocking a local population or migrating up and down the coast. The expanded tagging operations in 2026 will also provide vital information of the migratory dynamics of this currently unregulated species. When an angler lands a tagged sheepshead, it is advisable to release the fish. The acoustic tags not only provide meaningful data to understand this species’ behavior, but they are also quite expensive. Sutures on a fish’s belly are tell-tale signs of a sheepshead tagged with an acoustic tag.

Before you set your sights on stripers and tautog this fall, remember that sheepshead remain in the bays later than most anglers think. If you enjoy targeting this species, don’t give up too early. There are still plenty of opportunities in October for these sneaky convict fish to steal your bait.

Contributors:

Paul Ziajski

Owner, Great Bay Outfitters

Chase Wunder

Ph.D. Student, Rutgers University Marine Field Station (RUMFS)

Graduate Research Fellow, Jaques Cousteau National Estuarine Research Reserve (JC NERR)

Dr. Thomas M. Grothues (Ph.D.)

Director, Rutgers University Marine Field Station (RUMFS)

Research Coordinator, Jaques Cousteau National Estuarine Research Reserve (JC NERR)

Dr. Keith Dunton (Ph.D.)

Associate Professor

Monmouth University