Get Email Updates

Connecticut River Estuary: Haven for Juvenile Fish and Migratory Fish Highway

By Jenna Pirrotta, Northeast Regional Office Habitat Conservation Division

NOAA Fisheries Service Habitat staff is involved in ongoing efforts to help protect key habitats for juvenile and migrating fish that make their home in the Connecticut River. Due to its high species diversity and productive habitats, the Connecticut River estuary and tidal wetlands complex is listed as a “wetland of international importance,” as defined by the Ramsar Convention.


Large brackish marsh system in the Connecticut River estuary, Old Saybrook, CT.  Photo credit: NOAA Fisheries, Jenna Pirrotta.Connecticut River Estuary, Old Saybrook, CT.  Photo Credit: NOAA

The Connecticut River is the longest and widest river in New England,  flowing 410 miles from the Connecticut Lakes in northern New Hampshire into Long Island Sound in Connecticut.  It was formed at the end of the last ice age, more than 10,000 years ago.  The name was derived from the pronunciation of the Native American word “quinetucket,” which means “long tidal river.”  The Connecticut River estuary is the transiion zone formed where the river meets Long Island Sound.  It is a brackish system, home to a diverse group of fish and wildlife species.  

The Connecticut River and its estuary is an important migratory corridor  for many anadromous fish including river herring, Atlantic salmon, American shad, Atlantic and shortnose sturgeon and striped bass.  These are fish that spend most of their lives in the ocean and return to brackish waters and rivers to spawn.  In more saline areas of the estuary, small marsh fish such as bay anchovy and Atlantic silverside provide forage for larger commercially and recreationally important species such as winter flounder, summer flounder and bluefish.

Habitat Types 

The estuary contains vast areas of brackish tidal marsh, tidal flats, freshwater submerged aquatic vegetation (SAV), and shallow subtidal sandy habitats.  Several coves and tidal creeks form intricate patterns on the estuary’s shoreline and provide refuge for juvenile fish from the mainstem river waters.  These habitats support riverine food webs, and are critical to the successful production and growth of young migratory and estuarine fish that use estuaries as nurseries.  Brackish tidal marshes and SAV provide nutrients in the water column from decomposition of plants, which provides food  for young fish.  These habitats also filter nutrients, minimize shore erosion, improve water quality, and provide cover and forage areas for  young finfish.  Shallow water habitats provide cover for young fish from larger mobile predators.  

 Habitat Threats

Habitats in the Connecticut River estuary are threatened by human development through dredging, building of docks that fragment habitats, water quality impacts from vessel discharges, non-point source pollution (e.g., pesticides, chemicals, sediment etc.) from farms and urban runoff, sewage treatment plant discharges, water withdrawal, runoff from road and rail crossings, non-native plant invasion, and mosquito ditching.  “Mosquito ditching” is the digging of straight channels within marshes to drain ponded areas where mosquitos may breed.  It was done in the early 1900s and has since altered marsh habitats by eliminating marsh pools, which provide habitat for small marsh fish that eat mosquito larvae.  Threats to brackish marshes also come from adverse changes to river flow and changing sediment patterns driven by land clearing and other development in the watershed.

Phragmites/common reed invasion and dockside construction threaten saltmarsh. Photo credit: Nate Margarson, Environmental Protection Agency.Large brackish marsh system is threatened by Phragmites/common reed invasion and dock construction. Photo credit: NOAA. 

What We Do

“Our Habitat Team is working hard to protect important habitats within the Connecticut River estuary that plays a key role in supporting our nation’s fisheries,” said Lou Chiarella, assistant regional administrator, Habitat Conservation Division, Northeast.  

Our work entails coordinating with state and federal natural resource and regulatory agencies including the New England District Army Corps of Engineers, US Environmental Protection Agency, CT Department of Energy and Environment, and US Fish and Wildlife Service on various federally permitted projects.  We conduct environmental reviews and perform Essential Fish Habitat consultations on various  activities in the Connecticut River estuary.  Specifically, we provide conservation recommendations to permitting authorities to minimize impacts of human development from activities like dock construction, navigational dredging and bank stabilization activities on the habitats within the estuary.  Recommendations may include alternatives to minimize the impact of the project, time of year restrictions and best management practices, including the use of erosion controls to minimize sediment input into the water column or sensitive habitats.  With such varied threats facing the Connecticut River estuary, it is important to avoid and minimize impacts to these productive habitats.