Penobscot River Estuary Research Project

Understanding the importance of this complex environment for sea-run fish

Estuaries are complex environments for sea-run fish to navigate multiple times in their lives. The Penobscot River Estuary is no exception. Over the last two decades we have focused on investigating which sea-run fish are present at what times of year.  The following pages detail the background for this project, why it is important, and what we have found.

Maine’s rivers and streams are the home for the last remnant Atlantic Salmon in the United States, and populations in Maine have been critically low since the 1990s. Dams, overfishing, and pollution have cut these sea-run fish off from their spawning habitats and put stress on their population. While there have been major efforts to address the challenges that have caused declines, salmon and other sea-run fish numbers have not recovered. Statewide, roughly 1,000 adults return to Maine’s rivers in the spring. Most of these returns are to one system, the Penobscot River. 

Why the Penobscot River estuary is important to Atlantic Salmon

The life cycle of sea-run, or diadromous, fish involves at least two transitions between fresh and saltwater. Atlantic Salmon transition multiple times during their lifespan. They spend their first years in freshwater before migrating downstream as smolts, through the estuary, and out to the open ocean. Salmon from the Penobscot River watershed head to the Davis Strait between Labrador and Greenland more than 4,000 km away, a journey roughly the same distance as traveling from Maine to the Mexican border.  After spending 1-3 years in the North Atlantic, the salmon return as adults to the Penobscot River headwaters to spawn. Surviving adults cycle between feeding in the ocean and spawning in the rivers and streams, each time stopping in the estuary as they transition between environments.

A dynamic environment

The transition from headwaters to the ocean is challenging for a fish. As fish near the ocean, the waters turn saltier and colder. Atlantic Salmon smolts, which have been thriving in freshwater, are not immediately physiologically prepared for life out to sea. Time spent in the estuary, while short, is essential as it gives their bodies the time needed to physiologically change and adjust to new conditions.

The Penobscot River estuary in particular marks a complex environment. In the spring, smolts are emigrating out of the rivers at roughly the same time that adult Atlantic Salmon and alewife are returning. Schools of fish attract predators from the land and sea, making the journey through the estuary a gauntlet. Double crested cormorants and other birds hunt from above the waters, while seals and porpoises stalk fish from below. Recent studies show that this transition is a period of very high mortality with only about half of smolts surviving through that short time window.

The health of other sea-run fish populations also impacts Atlantic Salmon mortality. Historic records and production models estimate the Penobscot River used to be home to millions of alewives, a species of sea-run fish that are roughly the same size, shape, and color as Atlantic Salmon smolts. Considering these species utilize the estuary at roughly the same time, researchers hypothesize that the sheer number of alewives may reduce predation pressure on Atlantic Salmon. Healthy populations of Blueback herring and American Shad would have also been an alternative food source for estuarine predators in the past. Like Atlantic Salmon, however, other sea-run fish population numbers are historically low. As alewife, Blueback herring, and American Shad decline, predation pressure on Atlantic Salmon likely increases.  The idea that low abundance levels of one prey species may result in elevated levels of predation on another is called the prey buffer hypothesis.

An understudied area

Many of the interactions that impact Atlantic Salmon survival are thought to occur in or near the estuary. Yet, scientific monitoring in the Penobscot estuary has been scarce. Prior to our investigations that began in 2010, most Atlantic Salmon research and monitoring efforts focused on gathering data either upstream or offshore.

In the Penobscot River, Maine Department of Marine Resources (DMR) has monitored Atlantic Salmon migrations through fishways  at the Veazie dam from 1978 to 2013 and Milford dam since 2014. These efforts, however, have generated limited data on other species of sea-run fish that use the estuary. The information that is collected provides an indirect indication of those species’ abundance, distribution, and timing. 

Since 2000, studies in Penobscot Bay include a semi-annual inshore survey conducted by Maine DMR and the New Hampshire Fish and Game Department to document the distribution and relative abundance of marine resources. The method is bottom trawling designed to catch cod and lobster, not sea-run fish. Limited information about sea-run fish is collected.

What are we doing?

Given these data gaps, we conducted a multi-year survey to establish baseline information and to monitor changes in the Penobscot estuary starting in 2010. That same year, large-scale dam removal and restoration efforts began. Monitoring of this restoration effort has been extensive in freshwater (see Penobscot River Watershed Habitat Blueprint project). But, the estuary is where we see and can monitor the “ecological output” of changes upstream.

Our long-term goals are:

  • Provide a long-term data set to assess fish community structure and individual species abundance;
  • Provide a quantitative description of the predator and prey fields to assess the prey buffer hypothesis;
  • Provide a sampling platform to conduct species-specific studies and other ecological interactions occurring in the Penobscot estuary