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Fish and Ships Get Safe Harbor

This summer marks the end of an era for the waters around the Statue of Liberty. New York and New Jersey’s harbor deepening project will complete more than 20 years, 38 miles, and $1.6 billion of improvements to create a safe and efficient route for large container and cruise ships.

The harbor provides more than just access to ships. It’s found within the Hudson River estuary, home to many commercially and recreationally important fish; among them are bluefish, summer flounder, black sea bass, scup, and winter flounder.



The harbor serves marine terminals in New York and New Jersey, and supports 270,000 jobs each year. Credit: U.S. Army Corps of Engineers

A  Team Effort

This project was completed through a decades-long partnership between the U.S. Army Corps of Engineers (Corps) New York District, the Port Authority of New York and New Jersey, the States of New York and New Jersey, and NOAA Fisheries. The deepened harbor supports 270,000 jobs each year.

Protecting Essential Fish Habitat

NOAA Fisheries’ contribution to the project was to protect fish habitat that could be affected during dredging and port improvement activities. NOAA Fisheries gets this authority from the nation’s main fisheries law, the Magnuson-Stevens Fishery Conservation and Management Act. In 1996, the Magnuson Act established the need to identify and protect “essential fish habitat” (EFH) for all federally managed fisheries. The Magnuson Act also calls for NOAA Fisheries and other federal agencies to work together to minimize human-caused threats to fish habitats.

NOAA Fisheries has worked with the Corps for more than 30 years to conserve EFH during important maintenance dredging and port improvement projects. Federal agencies, like the Corps, work with NOAA Fisheries on all proposed actions authorized, funded, or undertaken that may adversely affect EFH. NOAA Fisheries provides advice and recommendations to federal agencies to minimize impacts to fish habitat.

Types of Habitat in the Harbor and Estuary

The New England and Mid-Atlantic Fishery Management Councils have identified and described EFH for each life stage for federally managed fish species living in this area.

One bottom fish gained signature status during the project. 

“There are so many federally managed fishery species within the harbor. When we drilled down and focused on things that don’t move or don’t get out of the way, we came down to winter flounder,” says regional EFH coordinator Karen Greene.

Winter flounder use the harbor’s sandy and muddy bottoms to spawn, or release their eggs. Credit: U.S. Army Corps of Engineers.

Commercial and recreational winter flounder landings are valued at over $1 billion. Winter flounder are a flatfish that use sandy and muddy bottoms to spawn, or release their eggs. Because these eggs are not buoyant and develop on the bottom, they are very vulnerable to dredging activities.

NOAA Fisheries recommended to the engineers which areas to steer clear of (shallow areas where winter flounder lay their eggs), and when to dredge (times of the year when eggs and larvae would not be present in the harbor).

“The recommendations were pretty conservative, but everyone agreed that was what was needed because we didn’t have great scientific data. It was incumbent upon the Corps to go out and get that data,” says Jenine Gallo from the Corps’ New York District.

Early Bird Gets Best Fish

NOAA Fisheries habitat specialists worked with the Corps early in the project to map out EFH and compare it to the areas that needed dredging.

“We had frequent meetings at the NOAA Sandy Hook Field Office and at the NY District Corps Office to try to work through some of the scheduling challenges and seasonal restrictions. We had to get very creative about how to dredge the area,” says Gallo.

The Corps tackled the complexity of fish habitat. “I remember the pencils and the rulers on the charts. The engineers were very good at thinking outside the box,” Greene says.

Opportunities for Data

The project’s parties agreed to long-term sampling to study the various fish species in the harbor. For winter flounder, the Corps monitored eggs, larvae, juveniles, and adults. They also characterized  sediments and invertebrate fauna  that are important attributes of fish habitat throughout the harbor,  including underwater video surveys, as a  pilot study,  to describe habitats both inside and adjacent to navigation channels.

These monitoring programs helped the Corps decide the best times to dredge.

The USACE and NOAA Fisheries worked together to research and protect EFH in the harbor. Credit: U.S. Army Corps of Engineers.

“I think we did some really unprecedented work collecting eggs and larval stages. We built an amazing data set from this long term monitoring. Heaven knows that most projects you’re involved in, if you get three years of data, boy, you’ve really won the game. But to have ten-plus years of data from this study, as scientists, we’re in awe of all this,” says Doug Clarke, an HDR contractor on the project.  

Benefits from Determination

The project’s meticulous, long-term studies have improved habitat protection and fishery management in the harbor.

“We collected eggs and larvae in the field. Then we looked at them under the microscope in the lab, where we were able to determine their stage of development. That helped us figure out where the winter flounder eggs were spawned, what types of habitats they used, and where they came from,” says David Davis, an HDR contractor.

The New England Fishery Management Council used the data to refine their EFH designations for winter flounder. Findings from the Corps-sponsored studies have also been published in numerous reports and scientific journals and presented to the scientific community at both local and international conferences.

Reflecting on Success

Heading into the harbor’s maintenance phase has given everyone a chance to reflect on the successes of the deepening project.

 “We’re still protecting EFH and still protecting those resources with the Corps. They get it,” says NOAA Fisheries’ Greene. “They and their partners were willing to invest in this research so that they could more effectively dredge the harbor while also protecting its natural resources.”

Gallo agrees. “We still have close collaboration with Karen and her team, the Port Authorities of New York and New Jersey, and the states on seeing this project through completion and how it transitions to the maintenance phase. It’s a long term relationship that will outlast Karen and me.”

Cumulatively, the efforts of this multi-agency partnership represent a prudent investment in filling knowledge gaps that will benefit efficient and environmentally sound dredging project management practices far into the future.

The harbor deepening project has begun transitioning from a Corps Civil Works construction deepening project to the Corps Operations Division for maintenance, as the planned depth for each navigation channel is achieved and a controlling depth report is issued. The final transition to maintenance work is expected to occur over the next several months and a project ribbon cutting ceremony is being planned to celebrate the completion of the construction of the USACE’s largest deep-draft navigation project. The project will leave a legacy of robust scientific data collection and analysis as well as strong coordination between the Corps and NOAA Fisheries.