The health of the Cape’s ecosystems and food webs depend on clean water. Our coastal waters, estuaries and embayments support valuable shellfish such as oysters, scallops, quahogs and mussels, as well as important finfish, such as winter flounder and striped bass. Freshwater ponds and streams support numerous fish and wildlife species, including important diadromous species such as river herring and American eels, which live in both fresh water and the ocean. A plethora of birds depend on the Cape’s tidal flats, salt marshes, quiet saltwater embayments and freshwater ponds as habitat for overwintering, a place to raise their young, or an important stop on their annual migration. It’s not a coincidence. The Cape’s water ecosystems provide a rich food source for all forms of wildlife, and people.

However, when water quality is degraded, so are the habitat values. Excess nitrogen and phosphorus from wastewater, stormwater runoff and fertilizer use fuel algal blooms that reduce the availability of oxygen in the water which aquatic organisms rely on. Climate change is impacting ecosystems in ways yet to be fully understood, but we do know that warming water temperature has serious implications for cold water fish species, like sea run brook trout, and is a contributing factor to more frequent toxic cyanobacteria blooms.

Learn more about Cyanobacteria

American Eel

American Eel

The American eel is a pretty amazing creature. For starters, it’s the only freshwater eel in North America and the only catadromous fish in North America. And yes, despite its body shape, it is a fish…

River Herring


The river herring of the northeast US include the alewife and the blueback herring. Herring are anadromous fish, which means they spend their adult life in the ocean and spawn in freshwater…

Striped Bass

Striped Bass

Atlantic Striped Bass are also known as rockfish, linesides, and stripers. The small stripers are called schoolies. They are a managed fish species and are wild caught from Maine to North Carolina and are also a species that are farmed…

Sea Run Brook Trout

Sea Run Brook Trout

Sea Run Brook Trout. This is the Cape’s only native trout. Cape Codders refer to them as “Salters”. They are an anadromous form of brook trout, which means they live part of their lives in marine waters, thus the…

The American Eel

Anguilla rostrata

The American Eel on Cape Cod from Association to Preserve Cape Cod on Vimeo.

The American eel is a pretty amazing creature. For starters, it’s the only freshwater eel in North America and the only catadromous fish in North America. And yes, despite its body shape, it is a fish. The eel is an ancient species that survived the glacial periods. It has a fascinating life story and we don’t even know the entire story. It’s all a bit of a mystery. But what we do know is that on Cape Cod, American eels can be found in freshwater ponds and streams. This is where they live their adult life, but they began their life thousands of miles away in the Sargasso Sea.

Identification. An eel is not a particularly beautiful creature because of its snake-like physique. They can vary in color, but have a dorsal fin and An eel lives its adult life in freshwater ponds where the males can grow up to 3 feet in length and the females can reach up to 5 feet, weighing up to 16lbs.

Habitat. They hide in shaded areas of ponds and prey on small fish, worms and other invertebrates. Some freshwater mussels depend on the eels to complete their life cycle.

Life Cycle. This migratory behavior is the opposite of the anadromous river herring Cape Codders know well that spend their adult life in the sea and journey upstream to freshwater ponds to spawn. The catadromous eel, when a mature adult will leave its freshwater habitat for the sea. And not just anywhere in the ocean. These eels will swim thousands of miles to the sea within the Atlantic Ocean the Sargasso Sea whose boundaries are created by ocean currents. The Sargasso Sea is named for the floating Sargassum seaweed that provides a safe haven nursery for many marine creatures and a rich ecosystem of food and shelter. Here, eels meet up with other eels and spawn, each female releasing tens of thousands of eggs.

There are many details of the eel life cycle which remain mysterious. What we know amounts to just an outline of understanding. We believe the spawning adults to be at least 5 years old, but some are believed to live to be 15 years or more. After spawning in the Sargasso Sea, the adults are thought to die. However, hundreds of millions of eggs hatch, and over the next year, the eel larvae drift in the Gulf Stream as they transform into a transparent form called the “glass eel”.

Somehow, these worm-sized larvae gravitate toward the shore in search of freshwater. Researchers have found that baby eels have crystals of magnetite in their brain, which is typical of other migrating species that provides sensitivity to the earth’s magnetic fields for navigation. As soon as springtime temperatures warm the water, the baby eels swim into estuaries to reach the freshwater ponds. In the estuaries, they begin to gain pigment and are referred to as elvers at about 2.5inches in length. At this stage, their sex is still undetermined. In the ponds they will mature to adults and live for many years before they return to the Sargasso Sea to create the next generation. A remarkable life history.

Ecological Value. Like herring, the eel is a keystone species that supports a wide variety of other animals as a food source in all its life stages. Even the life cycle of certain freshwater mussels depends on the eel.

The Problem. Eel populations are threatened due to degraded habitat from pollution and loss of the natural water connections between the ocean and freshwater ponds due to construction of dams and roadways, and from overfishing the species.

The Solution. To help recover the species, the harvesting of the baby eels as they re-enter fish runs has been prohibited in Massachusetts. Harvesting is still allowed in Maine and South Carolina where the small glass eels, about the size of large earthworms, are sold to Japan where they are grown out into adults for consumption. Some eels will return back to New England, but as a food item at your favorite sushi restaurant!

For more information: https://www.pbs.org/video/nature-mystery-eels/ ; https://www.mass.gov/service-details/learn-about-the-american-eel

River Herring

Alosa pseudoharengus and Alosa aestivalis

River Herring on Cape Cod from Association to Preserve Cape Cod on Vimeo.

River Herring. The river herring of the northeast US include the alewife (Alosa pseudoharengus) and the blueback herring (Alosa aestivalis). Herring are anadromous fish, which means they spend their adult life in the ocean and spawn in freshwater.

In the ocean, herring also fill an important niche. They are a food source for larger fish like striped bass and bluefish, dolphins and whales, and numerous other sea creatures. They are called a keystone species which is a species whose health and well-being reflects the overall state of the coastal ecosystem and can be an indicator of water quality problems.

Identification. Herring are small, streamlined, laterally compressed silvery fish in the family Clupeidae. The more than 200 species in this family share several distinguishing characteristics such as a single dorsal fin, no lateral line, and a protruding, bulldog-like lower jaw. Unlike many other fish, herring have soft fins that lack spines.

Life Cycle. As adults, river herring live in marine waters most of the year. They arrive to the Cape as early as mid-March, swimming through estuaries to where the freshwater meets the salt. There is some speculation that they return to the freshwater pond in which they were born and it is here they will spawn the next generation.

This is a harrowing trek as they swim the gauntlet of predators that over the millennia have cued into their arrival. The herring arrive when the gulls, osprey and herons are seeking nourishment for themselves and food for their young. Terrestrial predators include racoons and river otters. River herring are a crucial link in the food chain.

In general, spawning is initiated for alewives when the water temperature reaches 51 F (10.6 C). Alewives generally spawn in ponds. During spawning, the eggs settle and stick to gravel, stones, logs, or other objects. Unlike Pacific salmon that die after spawning, herring typically survive and move back to the ocean after spawning. Toward the end of summer and early fall, the young fish will head out of the ponds down the streams and into the estuaries when they are about 1-1/2 to 2-1/2 inches long and will eventually move to the open ocean to live their adult life.

Food. They are plankton-feeding (planktivores), typically traveling in large schools.

Historic Perspective. River herring have an important role in the history and coastal heritage of Cape Cod as well as other coastal communities from the Mid-Atlantic region up through New England. Towns with herring runs depended on the annual spring herring migration to harvest fish for food and sale, and herring contributed to the local economy. Native Americans also harvested herring for food. The Wampanoag culture and the herring are intertwined.

Less than a lifetime ago, the streams and rivers of Cape Cod were thick with river herring in spring. But river herring populations have been declining in the mid-Atlantic and Northeast coastal regions for several decades. For example, in the 1920s there were a million fish in the Coonamessett River which in recent years became less than 30,000. By the 1990s, the MA Department of Marine Fisheries knew there was something wrong with the herring population and in 2005 declared a moratorium on taking or catching any river herring in Massachusetts.

Habitat. River herring need a variety of habitats for spawning, rearing, and transitioning to and from saltwater. They are not selective of pond bottom which can include gravel, detritus, and submerged aquatic vegetation.

Threats. The decline in river herring is symptomatic of environmental problems that are impacting other fish, wildlife and whole ecosystems. Reasons for their decline include development that has introduced barriers to fish passage, like roadways that obstruct natural water flow and alterations dues to historic agricultural activities that closed off the natural flowing water connection from fresh to salt water.

Water withdrawals and diversion change stream paths, depth of water and flow. Warm temperatures stress fish and sometimes result in mortality. Improper management of water control during low stream flows can result in higher water temperatures than normal and result in less freshwater input to estuaries which are important nursery areas for young herring as they make their way out to sea.

Habitat loss due to development degradation of estuarine systems and quiescent ponds from alteration, excess nutrients and pollution. Water quality is declining due to pollution from septic systems, stormwater runoff and fertilizer use, causing acceleration of phytoplankton growth and when it dies, the bacteria that decomposes the microalgae consumes oxygen. This results in reduced dissolved oxygen, stressing fish and even resulting in fish kills.

Predation by wildlife, while a natural part of the food web, can be thrown off balance by land use activities that favor species, either intentionally or not. Poaching by humans despite the moratorium on taking herring is an annual occurrence. Only the Wampanoags through their tribal rights are permitted harvest herring in keeping with their cultural traditions.

A potential cause of the significant decrease in herring returning to spawn has been the overfishing and bycatch at sea. There was an effort by the Cape Cod Commercial Fishermen’s Alliance to advocate for a buffer zone for mid-water trawling that they feel is contributing to the reduction in river herring populations. As of February 2019, the National Marine Fisheries placed a reduced quota on the amount of Atlantic herring that can be caught, however this does not address river herring lost to bycatch.

The impacts of climate change include changes in precipitation and increased water temperature that changes the ecological balance of the pond and streams will also impact future generations of herring.

The Solution. Protect herring populations by

  • Insuring healthy estuaries, streams and ponds, and address nutrient overload from septic systems, stormwater runoff and fertilizers
  • Using best practices when recreating on ponds and for land use around ponds and within their watersheds
  • Support monitoring efforts and volunteer to count herring as they make their way to spawning grounds
  • Mitigating impact of groundwater withdrawals
  • Managing outflows from ponds during critical periods with this fish species in mind
    Removing barriers to fish passage like dams and restore natural water flow where possible
  • Be concerned about chemicals of emerging concern (CEC’s) entering our groundwater and surface waters through wastewater, particularly endocrine disruptors
  • Be mindful of the threats of climate change impacts
  • Advocate for appropriate fishery management policies to reduce bycatch

For more information on herring:

A Guide to Viewing River Herring in Coastal Massachusetts
Fish Restoration Fact Sheet

Atlantic Striped Bass

Morone saxatilis

Atlantic Striped Bass are also known as rockfish, linesides, and stripers. The small stripers are called schoolies. They are a managed fish species and are wild caught from Maine to North Carolina and are also a species that are farmed. Striped bass are a highly sought-after fish by both recreational and commercial fishermen. Any Massachusetts resident or non-resident may fish for striped bass but either a recreational or commercial permit is required to do so.

Identification. Striped bass have stout bodies with seven to eight continuous horizontal stripes on each side, from their gills to their tail. They are light green, olive, steel blue, black, or brown on top, with a white or silver iridescent underside. Females are larger than males.

Habitat. Striped bass live their adult lives at sea and return to rivers to spawn.

Food. Striped bass have been known to eat anything that swims, crawls or floats, even each other. However, the diet of the striped bass consists almost entirely of other finfish. They prefer menhaden, silversides and anchovies.
The larvae feed primarily on zooplankton and water fleas. After they hatch, the quarter-inch fish are attached to a heavy yolk sac, which provides them necessary nourishment for four or five days, then the fry begin to feed on small crustaceans. As they grow, their diet expands to include insect larvae, other larval fish, small shrimp and amphipods.

Life Expectancy. Striped bass can live at least 30 years and can grow to over four feet in length. Males are sexually mature between the ages of 2 and 4 years old and females reproduce when they are 4 to 8 years old. The small striped bass are fed on by larger fish-eating fish like bluefish, cod and hake. The adults are eaten by seals and sharks.

Reproduction. The migratory behavior of coastal striped bass is more complex than those of most other anadromous fish, which spend most of their adult lives in the ocean but migrate up rivers and streams to spawn. The seasonal movements of striped bass depend upon the age, sex, degree of maturity and the river in which they were born.

The Chesapeake Bay is the primary location for spawning activity and nursery area for the Atlantic Striped Bass population. Spawning activity also occurs in the Roanoke River/Albemarle Sound watershed in North Carolina and the Hudson River in New York.

In late winter mature striped bass begin to move from the Atlantic Ocean into tidal freshwater to spawn. Spawning is triggered by an increase in water temperature as well as salinity levels and generally occurs in April, May and early June in the Chesapeake Bay tributaries, Roanoke River and Hudson River. The fertilized eggs are transported downstream. The bass larvae require moving water, to enable them to remain suspended in the oxygen-rich region of the water column. Without the moving water, the developing baby bass larvae will sink to the bottom and will not survive because they will be deprived of adequate oxygen. If striped bass are found in reservoirs or lakes, it is because state fishery departments stock these waters. Natural reproduction cannot occur in still waters. Striped Bass have an innate sense of finding the right water before spawning.

Shortly after spawning, adult fish return to the ocean. This is when many move north to spend the summer and early fall months in the nearshore waters of New England. In late fall and early winter, they migrate south again.
Historic Accounts. In 1634, William Wood, in his New England’s Prospect, called the striped bass,

one of the best fishes in the Country . . . a delicate, fine, fat, taste fish…. The English at the top of an high water do crosse the creek with long seines or bass nets which stop the fish; and the water ebbing from them, they are left on the dry grounds, sometimes two or three thousand at a set, which are salted up against winter, or distributed to such as have present occasion either to spend them in their homes or use them for their grounds.

By 1639 it was observed that the fishery was significantly depleted due to overfishing and Massachusetts took regulatory steps and forbade the use of striped bass as fertilizer. This bold first step led to the eventual passage of the National Environmental Policy Act in 1969, the precursor to Magnuson-Stevens and regional fisheries legislation.

The Pilgrims also caught them with hook and line,

the fisherman taking a great cod line to which he fasteneth a peece of lobster and threwes it into the sea. The rockfish biting at it, he pulls her to him and knockes her on the head with a sticke.”.
(Bigelow and Schroeder, “Fishes of the Gulf of Maine”)

In 1670, the Plymouth Colony started a free school with income from the striped bass fisheries, becoming the first public school in America.

Striped bass were the subject of the first fish-stocking efforts following settlers to the west coast. In 1879 and again in 1881, Dr. Livingston Stone of the United States Fish Commission (a forerunner of U.S. Fish and Wildlife), began transporting striped bass from New Jersey to the San Francisco Bay. In milk cans and wooden barrels, the water was first agitated by hand and then refreshed to keep oxygen in the water. Later efforts employed a crude oxygenation system to keep the fish alive on their way across the country. The striper is now one of California’s top-ranking sport fish.

Threats. Striped bass populations have been threatened by overfishing, illegal take, exotic aquatic organisms and obstructions to natural hydrologic flow like dams that limit areas to spawn.

For more information on Striped Bass:

Sea Run Brook Trout

Salvelinus fontinalis

Sea Run Brook Trout

Sea Run Brook Trout. This is the Cape’s only native trout. Cape Codders refer to them as “Salters”. They are an anadromous form of brook trout, which means they live part of their lives in marine waters, thus the nickname Salters.

Identification. Technically sea run brookies are not a true trout. They are a char which is a subgroup of the salmon family. They are distinguished from other trout and salmon by the absence of teeth in the roof of the mouth and other physical attributes. They are beautifully colored, speckled with lighter colored spots of orange. It is the silver sheen of a brook trout’s skin that indicates it has spent time in salt water. It has been out to sea or at very least the estuary where it was enticed by the abundance of food available in the estuarine system.

Habitat. As sea level rose after the glaciers retreated, long fingers of cold water streams carved valleys as they flowed to the ocean. These cold groundwater-fed streams became excellent habitat for brook trout. Brook trout on Cape Cod are at the most southern part of their range as they require cold water where 50 degree water temperature is optimum.
Forested stream edges that include a jumble of tree roots and overhanging vegetation is critical to brook trout. The shade of vegetation helps moderate the temperature of the water. As temperatures go up, the fish get stressed and at 67 degrees they stop growing. There is much we do not know about the sea run brook trout, but we do know that 78 degrees will kill them.

Food. They are opportunists and will eat small aquatic and terrestrial invertebrates such as caddisflies, mayfly and damselfly larvae, flying insects, water beetles, snails, worms, whatever they can get their mouths on. In fast running streams, fallen logs and stream debris provide excellent feeding areas as well as cover from predators.

Life Expectancy. At a year of age, they are about 4 inches long. A 9 inch fish has been growing for at least three years. Brook trout are more plentiful in the streams in the western part of MA, but here on the Cape populations are slim due to many factors affecting their habitat. On Cape Cod, brook trout are a short-lived species and may live to only about 3-4yrs. Trout are mainly predated upon by osprey, herons and river otters.

Reproduction. Typically spawning in late October to early November. The female scours out a nest in the gravelling bottom, depositing her eggs that incubate in the gravel over the winter and hatch in late Jan to Feb. The spawning areas are very specific, where the edge of the bank meets the river and where there is upwelling spring water, substrate of sand and gravel. After hatching, they seek the marginal areas where water velocity is low.

Historic Accounts. Oral legends of the Wampanoag document abundant populations of the fish. Written historic accounts from John Rowe in the 1700s also speak to the plentiful fish and their much larger size. He documented catching several trout 18 inches in length, a size which is unheard of today.

Threats. Streams have been lost due to our development of the land. For example, two streams, the Monument River that originally flowed into Buzzards Bay and the Scussett River, would have been prime habitat for salters. These were both lost with the construction of the Cape Cod canal.

  • Other development, like dams and mills, created impediments to the movement and passage of sea run brook trout.
  • Road crossings often restrict the natural water flow.
  • Withdrawals of groundwater can reduce stream flow.
  • Removal of woody debris in the stream removes critically important protective cover for the trout. Logs and overhanging vegetation create cold pockets where fish can hold up in warmer days and hide from predators.
  • Good intentions of increasing habitat for ospreys has had unintended consequences for the brookies, giving these predators from above an unfair advantage.
  • Water quality impacts from wastewater, stormwater and fertilizers. Excess nutrients have changed the balance of natural systems from aquatic vegetation dominated ponds to one dominated by algae and cyanobacteria. Pollution has consequences yet to be fully understood.
  • The disruption of our climate is causing increased summer temperatures and warming of the waters.

The Solution. Protect existing trout populations by

  • Leaving and/or restoring the woody vegetation along both sides of streams and enhancing these riparian zones
  • Insure healthy estuaries and eel grass beds that provide valuable feeding areas
  • Mitigate impact of groundwater withdrawals
  • Monitor temperatures and flows to gain understanding of what is happening
  • Manage outflows from ponds during critical periods with these cold water fish species in mind
  • Remove barriers to fish passage like dams and restore natural water flow where possible
  • Be concerned about chemicals of emerging concern (CEC’s) entering our groundwater and surface waters through wastewater, particularly endocrine disruptors
    Be mindful of the threats of climate change impacts

Sea Run Brook Trout need

  • Woody debris
  • Vegetated banks
  • Overhanging vegetation
  • Shaded waters
  • Coldwater refugia – cold pockets of upwelling freshwater
  • Unobstructed water connections
  • Properly controlled water management with their needs in mind

For more information on Sea Run Brook Trout:

Sea Run Brook Trout Coalition
Fish Run Restoration Fact Sheet
Wild Brook Trout Mapping Tools


APCC’s Cyanobacteria Program 2020 from Association to Preserve Cape Cod on Vimeo.

What are cyanobacteria? Cyanobacteria are single-celled organisms commonly found in the phytoplankton community of aquatic ecosystems like the Cape’s freshwater ponds. They are ancient organisms with the ability to photosynthesize and attributed with creating the first oxygen. Cyanobacteria, also referred to as blue-green algae, are an important part of aquatic food webs. The presence of cyanobacteria is natural and important and there are lots of different kinds of cyanobacteria (PDF) that require a microscope for identification.

Cyanobacteria blooms & cyanotoxins. An overabundant growth of cyanobacteria is called a bloom, and depending on the species of cyanobacteria, cyanotoxins may be released. Often referred to as HCBs (harmful cyanobacteria blooms), blooms are triggered by excessive nutrients and warm temperature. Common cyanotoxins include:

  • Dermatoxin – A toxin that is a skin irritant. The most commonly occurring dermatoxin, lipopolysaccharide, is unregulated by the state.
  • Hepatotoxin – A toxin that can cause liver damage.
  • Microcystin – A type of hepatotoxin that can cause liver damage and is the primary cyanotoxin regulated by the Massachusetts Department of Public Health.
  • Neurotoxin – A toxin that can cause neurological damage. Anatoxin and beta-N-methyl amino-L-alanine (BMAA) are known neurotoxins that are unregulated by the state but are currently being studied by cyanobacteria researchers.

Exposure to cyanotoxins can have serious health implications for wildlife, pets, and humans. Most at risk are our dogs and children who, because of their small size, are more susceptible to the cyanotoxins in lower concentrations. Dogs can ingest cyanotoxins from drinking pond water or from grooming their fur after swimming.

What if I encounter a suspected bloom? Guidance from MA Department of Public Health advises the public to AVOID CONTACT with pond water that is suspicious looking because it is discolored or has a strong odor. If you can, take a picture, noting the date and time and provide the information to the town health department. The Association to Preserve Cape Cod, working with its many partners, maintains an interactive online map during the sampling season, June through October. The map provides the public with the pond’s status using a three-tiered system based on sampling results. When blooms are observed, the relevant local health department is notified. It is the town’s responsibility to then post warnings or beach closures as it deems appropriate.

Are ecosystems affected by cyanobacteria blooms and their toxins? Our local knowledge of the impacts from cyanobacteria blooms and cyanotoxins to ecosystems and food webs is limited. Research on juvenile herring in a pond in Brewster in 2019 by scientist and researcher Nancy Leland revealed that herring fed upon cyanobacteria almost exclusively during mid-summer. Understanding if this diet is affecting herring survival may help explain why herring populations on the Cape are still low.

Due to the Cape’s highly permeable sandy soils, most of its nearly 1,000 freshwater ponds and lakes are vulnerable to nutrient pollution from land uses and septic systems. The hydrological connection of our ponds to groundwater and the network of ponds, streams—many of which are herring runs—and estuaries provides a potential conduit for physical transport of cyanobacteria and their toxins.

However, additional monitoring data is needed to establish the degree to which transport of cyanobacteria from freshwater ponds downstream to estuaries is happening, and to determine if coastal ecosystems, water quality, and herring populations are significantly affected as suspected.