 
Hudson RiverNet: News from the Hudson River Estuary Management Program
In this issue:
Estuaries are among the most productive of Earth's ecosystems, and the Hudson River estuary is no exception. The Hudson's signature migratory and resident species—Atlantic
sturgeon, river
herring, striped
bass, blue
crab, and shortnose
sturgeon—depend on rare and important tidal habitat for spawning, feeding, and over-wintering. The Hudson
River Estuary Action Agenda 2021-2025 establishes specific measures to conserve, protect, and restore these signature species and their valuable habitat.
DEC's
Hudson and Delaware River Marine Fisheries staff have been managing the migratory and resident fishes of the estuary since the 1980s through numerous long-term monitoring surveys. Long-term data are extremely valuable for documenting population trends
over time, as they can reveal patterns in abundance not evident from single-survey events or short-term studies. Migratory species are managed in collaboration with other coastal states through the Atlantic
States Marine Fisheries Commission (ASMFC). The status of each major species has been very dynamic, influenced by local and coastal conditions. Read about some of this year's significant research findings and new developments in this newsletter.
During the annual haul seine, Hudson River Fisheries biologists count, weigh, and measure spawning striped bass as an indicator of population abundance.
New research estimates the population of endangered shortnose sturgeon in
the Hudson River to be nearly 70,000 individuals, likely making it the largest population of sturgeon anywhere in the world.
Shortnose sturgeon,
once abundant in rivers along the Atlantic coast, declined dramatically as the result of overfishing and habitat degradation, leading to their listing under the Federal 1973
Endangered Species Act. DEC's Hudson River marine biologists initial population survey, conducted to develop recommendations for managing the recovery of this species, estimated only about 6,000 adults. A second population study in the 1990s showed a substantial
increase, indicating that the Hudson River population might be among the largest in the world.
In spring 2021, DEC’s
Hudson and Delaware Marine Fisheries, in partnership with USGS
Eastern Ecological Science Center (EESC), Cornell University, University of Delaware, and Delaware State University, embarked on a large-scale project to update estimates for the Hudson’s
shortnose sturgeon population using acoustic telemetry and side-scan sonar. Acoustic telemetry uses stationary receivers
to detect signals emitted from tagged marine species such as sturgeon. Side-scan sonar uses sound waves to create an image of
the river floor and objects in the water column.
Before launching the full study, the team tested the effectiveness of side-scan sonar to detect this small sturgeon by imaging wooden sturgeon models of various sizes. The results showed that sonar could reliably detect fish as small as 1.5 feet - a critical
benchmark for counting shortnose sturgeon.
One hundred adult shortnose sturgeon were first netted on the spawning grounds in Albany and surgically implanted with long-lived (10-year) acoustic transmitters, that are detected on a river-wide array of acoustic receivers as the fish move throughout the
Hudson River estuary. The receivers store the unique tag number and the date and time that a fish swims past a receiver (like E-Z Pass for sturgeon).
During the winter, staff used side-scan sonar to image and count individual shortnose sturgeon at their major overwintering area. At the same time, directed gillnet sampling of these sites was carried out to effectively substantiate the sonar surveys. The nets
primarily caught shortnose sturgeon during these surveys, confirming that the fish on the side-scan images where shortnose sturgeon. The sonar derived estimates were mathematically merged with the river-wide telemetry data to estimate the proportion of individual
fish in the overwintering areas, and by extension, in the overall Hudson River.
Side-scan sonar data was collected in the overwintering area in winter from 2021-2023. A large amount of data and thousands of images coupled with dense aggregations of sturgeon in relatively small areas proved challenging to analyze.
A collaborative team led by USGS Eastern Ecological Science Center developed a new statistical tool that combines data from side-scan sonar surveys, processed using artificial intelligence, with telemetry. New methods that use automated image processing analysis,
followed by the application of machine learning helped speed up the process.
The findings, published in a recent
scientific article in the Canadian Journal of Fisheries and Aquatic Sciences, highlight both the resilience of shortnose sturgeon
as well as the sturgeons' vulnerability to local disturbances. More than 40 percent of the population congregates in a small overwintering habitat, which coincides with an area of high human activity, including commercial shipping and underwater construction.
The study was conducted in partnership with Cornell University, EESC, University of Delaware, Delaware State University, and DEC with funding from the
Hudson River Foundation and DEC’s Hudson
River Estuary Management Program through New York State’s Environmental
Protection Fund. All shortnose sturgeon were collected and tagged under a National Marine Fisheries Service Endangered Species Act Research permit #20340.
An endangered shortnose sturgeon is carefully removed from a net.
In 2021, during routine fish monitoring, DEC Hudson River fisheries staff captured four invasive round gobies downstream of the Troy Federal Dam, marking the species’
first known presence in the Hudson. By the end of the year, DEC had documented 112 round gobies in areas as far south as Poughkeepsie, raising alarms about the potential ecological, recreational, and economic impacts on the river and its tributaries.
Round gobies are aggressive bottom-dwelling fish that reproduce rapidly and have voracious appetites, consuming small invertebrates, mussels, and the eggs of native species, including popular sportfish like smallmouth bass and walleye. Although the fish had
already spread to several New York watersheds, including the Erie Canal and Mohawk River, the goby’s arrival in the Hudson raised concerns about their competition with native species, as well as their potential to spread diseases such as viral hemorrhagic
septicemia (VHS) and avian botulism, seen in other Great Lakes regions.
Given the round goby’s disruptive potential, Hudson River marine biologists launched several initiatives to research the spread of goby and their potential impacts. Since 2022, biologists have been using environmental DNA (eDNA) sampling and other monitoring
methods to track the spread of goby throughout the tidal Hudson River. Two ongoing studies in collaboration with SUNY Oswego are also exploring the threat of predation from goby on sturgeon and other migratory species (striped bass, American shad) and estimate
changes in round goby population sizes using genetic techniques.
By 2023, research had expanded to include experiments on the ability of round goby to survive in brackish and saltwater environments. Studies led by Cornell University in collaboration with DEC focused on the species’ salinity tolerance, a key question for
understanding how far the goby could spread in the Hudson River estuary and beyond, into marine environments like New York Harbor. The research revealed that the goby could seasonally survive in waters with salinity levels similar to those in the Harbor, suggesting
that it could potentially colonize the entire Hudson River watershed and disrupt marine ecosystems.
A significant, collaborative management response also has also been implemented by DEC, the New York Power Authority, and the New York State Canal Corporation through the development of a rapid response plan aimed at preventing the spread of the goby through
the Champlain Canal into Lake Champlain. DEC and USGS have been using traditional fish sampling techniques and eDNA to monitor the presence of goby in the Champlain Canal. The monitoring data are used to execute a series of adaptive actions as outlined in
a trigger action response plan (TARP). The TARP includes various mitigation strategies, such as double draining locks and canal traffic restrictions, to reduce the likelihood of round goby reaching Lake Champlain.
DEC remains committed to monitoring and mitigating the spread of round goby in the Hudson River and its tributaries. With ongoing research, collaboration with partner agencies, and a comprehensive approach to invasive species management, DEC is working to protect
the Hudson River and the communities that rely on it.
2025 marks the third consecutive year of poor catches of juvenile
river herring and
American shad in the Hudson River estuary, with numbers significantly below established thresholds for recovery. Three alosine species migrate into the Hudson River. Alewife, (Alosa pseudoharengus) and blueback herring
(Alosa aestivalis) are forage fish that serve as key food sources for migratory striped bass and other fish. American shad
(Alosa sapidissima) is the largest fish in the Alosa genus and was an important fish for sustenance and recreational angling until the stock collapsed in the 2000s, and all shad fisheries closed in the Hudson.
Alosine species spend most of their lives in coastal Atlantic waters but migrate into the Hudson River and tributaries to spawn each spring. Adults return to the ocean after laying their eggs, while juveniles remain and grow, moving downriver to join the migratory
stock. During the early life-stages as eggs and larval fish, juvenile river herring survival is impacted by changing temperatures, habitat and food availability, water quality, and predation among other environmental variables. Females can lay over 100,000
eggs or more in a season, but less than 1% will survive to adulthood.
DEC’s Hudson River fisheries staff monitors the abundance of adults and young-of-year (YOY) fish to detect population changes, as river herring rely on the estuary during multiple life stages. The annual beach seine survey monitors young-of-year alosine species
from June to October each year at 29 fixed stations between Newburgh and Albany.
The geometric mean catch per unit effort, or average number of fish caught in each net, is calculated as the juvenile abundance index (JAI), which shows a relative measure of reproductive success since DEC began the survey in 1980. While the JAI for American
shad has been well below the limit reference point since the 2000s stock collapse, the JAI for alewife and blueback herring has also remained concerningly low for the past three years.
Limited recreational and commercial fisheries are permitted in the Hudson for river herring and managed under a
Sustainable Fishery Management Plan (SFMP), which is approved by the
Atlantic States Marine Fisheries Commission (ASMFC). All fisheries for American shad on the Hudson river are closed, with possession prohibited. The
Recovery Plan for Hudson River American Shad (PDF) guides shad management in the river.
Measuring juvenile shad netted during the beach seine near Coxsackie.
The American eel (Anguilla rostrata) is an ecologically important species in the Hudson River estuary, as it is both predator and prey. The Atlantic States Marine Fisheries Commission 2023 benchmark stock assessment determined that the population remains
stable, but at a historic low in U.S. waters. This likely is due to a combination of factors such as historical overfishing, habitat loss, and water pollution.
American eel spawn in the Sargasso Sea and after the eggs hatch, they drift on ocean currents in a life stage known as “leptocephali”. Over the course of about a year of drifting and transitioning, they grow into another life stage known as “glass” eels and
begin making their way into estuaries and up rivers and streams. They then become a pigmented “elver” and as they grow larger, they turn into what is known as a “yellow” eel. They will spend most of their life in the yellow phase, growing larger and maturing
for years, until they ultimately become mature “silver” eels. When they are silver, they will leave their fresh and brackish water habitats to return to the Sargasso Sea to spawn and the cycle will begin all over again.
There is some knowledge about their life in freshwater, but little is known about the silver eel and what prompts them to embark on their long journey back to the Sargasso Sea. To better understand their movement, fisheries biologists tagged American eels in
three tributaries of the Hudson River estuary. Through electrofishing and netting, 50 eels were captured and acoustically tagged in the fall of 2024; another 50 eels are now being tagged. Acoustic receivers throughout the estuary record the location and time
when a tagged fish moves by them. Fisheries biologists analyze this data to piece together the movements of the fish, helping improve understanding of the final life-stage of American eels. Identifying potential important environmental triggers for the timing
of their migration to the sea as well as routes they take as they leave the estuary, will help protect eel habitat, particularly during the time this important species makes the vulnerable journey back to the Sargasso Sea to spawn.
Biologist Jess Best surgically implants an acoustic tag in a silver eel.
For more than a decade, the Hudson River Fisheries Unit has partnered with Delaware State University to track the incredible journeys of Atlantic sturgeon. Since 2009, we’ve maintained an acoustic array in the Hudson River—a network of underwater receivers
that detect tagged fish as they swim past. Many of these sturgeon originally were tagged by Delaware State researchers off the coast of Delaware, but the story often begins much closer to home: most of them were born right here in the Hudson.
These detections act like check-ins on a travel map, showing us when and where sturgeon move throughout the river. By piecing together these patterns, scientists can better understand migration timing, critical habitats, and areas that need extra protection
to support the recovery of this ancient fish.
Working with the U.S. Geological Survey and partners along the East Coast, we’ve learned that Hudson River Atlantic sturgeon lead remarkable lives. After spending just a short time in the river as juveniles, they set off on epic migrations, traveling from Florida
to Canada and exploring many freshwater rivers along the way. When it’s time to spawn, most return to the Hudson, gathering near Hyde Park. Others head farther north to Catskill, a secondary but important area that we believe fish may be using for spawning.
By studying whether Atlantic sturgeon always return to the same spots—or switch between them—we gain insight into their survival strategies. Each new discovery helps managers protect the Hudson’s sturgeon and ensure that future generations will continue to
witness these giants of the river.
Detections from the Hudson River acoustic array—and from partner arrays along the coast—have revealed just how far Atlantic sturgeon travel and where they may be running into trouble. While completing their migrations, many individuals pass through heavily
used waterways where human activities such as dredging, marine construction, and ship traffic can pose serious risks. These detections not only expand our understanding of sturgeon movement but also highlight the importance of protecting migration corridors
and reducing threats like ship strikes to support the recovery of this endangered species.
A marine biologist surgically implants an acoustic tag in an Atlantic Sturgeon. National Marine Fisheries Service Endangered Species Act Research permit #20340.
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