Often Misunderstood Estuaries Underpin Environment’s Health

April 25, 2018


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A wetland area in the Chesapeake Bay, a complex estuary into which at least 11 major rivers flow. The bay drains parts of six states, serving as a catchment basin for huge urban and agricultural areas that bring damaging runoff pollution to its historically important fisheries. Photo: U.S. EPA.

Backgrounder: Often Misunderstood Estuaries Underpin Environment’s Health

By Joseph A. Davis

Estuaries. In much of the United States and Canada, good environmental reporting means keeping up with these little understood, little attended, but highly valuable and at-risk waters.

To define an “estuary” simply as a tidal widening of a river’s mouth as it meets the sea does not do it justice. Nor does describing it as a transition zone between fresh and saltwater.

Consider the Chesapeake Bay system. The Chesapeake is way bigger and more complex than all that. At least 11 major rivers flow into it and many more small ones. It drains parts of six states. It hosts several major ports.

And the United States and Canada have many other major estuaries: Alaska’s Cook Inlet, Puget Sound (Salish Sea), San Francisco Bay, the Sacramento-San Joaquin River Delta, Boston Harbor, Long Island Sound, the Lower Hudson, Narragansett Bay, Delaware Bay, Albemarle Sound, Pamlico Sound, Mobile Bay, Tampa Bay and more.


These waters are of huge economic,

ecological and even spiritual importance.

These values are usually in conflict.


While it’s true that many estuaries are defined by a gradient of salinity between fresh and marine waters, there are other coastal waters, often salty, that also need special care and attention no matter what we (or geographers) call them.

Is Alaska’s Prince William Sound an estuary, for example? And much of the Gulf and Atlantic coasts involves complex structures of barrier islands with sheltered waters (sometimes called “sounds”) behind them. They may be tidal but have different salinity than the ocean, and often abound in ecologically important wetlands and marshes. Can we lump these in with estuaries?

Chesapeake an example of estuaries’ travails

These waters — bays, gulfs, sounds, inlets, etc. (let us call them all “estuaries” for now) — are of huge economic, ecological and even spiritual importance. These values are usually in conflict, and the physical geography is often being changed by natural and human forces. They frequently cross or transcend political boundaries.

Look again at the Chesapeake. Historically, huge fisheries have thrived in it that have sustained humans and other animals. For instance, before Europeans arrived, it supported huge oyster populations that made life good for native tribes. But centuries of overharvesting, along with environmental insults, have decimated Chesapeake oysters, and the struggle now is to bring them back.

In another example, many of the striped bass, or rockfish, along the Atlantic coast are hatched in the Chesapeake, along with other estuaries. But overharvesting by commercial and sport fishers, along with environmental factors, led to a severe decline in the 1970s and ’80s. Congress then passed the Atlantic Striped Bass Conservation Act in 1984, and some key Bay states imposed fishing moratoriums. After years of effort, the striped bass fishery is largely restored.

The Chesapeake is lined with endlessly ramifying, or branching, channels and salt marshes, where vegetation, insects, crustaceans, mollusks and fish flourish, along with the many bird species that feed on them. Yet it is also home to some major ports — Norfolk, Newport News, Hopewell, Baltimore and Havre De Grace among them — and the industries they support. Its catchment basin also includes huge urban and agricultural areas, which contribute lots of runoff pollution.

Some key estuary issues to track

As you explore the concerns and issues surrounding your own estuary, you will discover that each estuary is unique and that the biggest issues vary. But there are some common threads that apply to most. Among them:

  • Pollution. The quality of estuary waters matters a lot to all the life-forms that dwell, feed and breed in them. Many of the biggest industrial pollution discharges have been controlled. But problems remain with diffuse (“nonpoint”) runoff from city streets and farm fields. Stormwater contains nutrients like nitrogen and phosphorus from farm fields that promote the algae growth that can choke estuaries. It also contains oil, pesticides and other chemical pollutants that can affect the food chain. Contamination from sewage can spoil seafood and cause disease.
  • Fishing. Most estuaries support sport and commercial fishing, and overfishing must be controlled if these fisheries are to continue. States and regional authorities do regulate fishing to some extent. But is it enough? Both commercial fishers and sport fishers lobby hard to raise catch quotas — sometimes with only short-term self-interest in mind. To be robust, fish populations need food and habitat, too.
  • Shipping. Most of the larger estuaries have harbors and host some kind of shipping. That engenders pollution — whether of the chronic, low-level kind or the catastrophic kind exemplified by the Exxon Valdez spill of 1989. Laws prohibit discharge of pollution in U.S. estuarine waters, but the U.S. Coast Guard does not always succeed in catching culprits. Dredging for shipping channels produces sediment (sometimes polluted) which presents many challenges.
  • Changes in water flow. The ecological balance — and rhythm — in most estuaries hinges on many flows. The tidal flows of saltwater. The freshwater flows from tributary streams. All kinds of manmade structures and activities, like dams and harbors, can modify those flows. Also, nature poses challenges from things like drought, floods and ice. Some of these, like dam construction and management, can be controlled.
  • Invasive species. Invasive species in an estuary system (think land as well as water) can cause all kinds of havoc. In the worst cases, the lack of established natural predators allows them to multiply quickly and destructively. In the Chesapeake system, for example, blue and flathead catfish are unwelcome. The large water-based rodents known as nutria are now threatening to invade the Sacramento-San Joaquin Delta. They burrow into structures like levees.
  • Algal blooms. You may have heard of the infamous “red tides” that typically plague some Florida estuarine waters. They can poison people, animals and marine life. These are a kind of harmful algal bloom. Two factors that kick them into high gear are excess nutrients and high water temperatures. Estuaries are more vulnerable to harmful algal blooms. Controlling nutrients helps reduce their severity and frequency.
  • Development and habitat loss. That beautiful saltwater marsh you love to search for birds is the epitome of why estuaries are valuable. Estuaries host all kinds of landforms and water conditions that nurture whole ecosystems. But what happens when the salt marsh is turned into a marina? Or when the dune is topped with beach homes? Only a few federal programs (like the National Flood Insurance Program) can impact such habitat loss. Much of the responsibility lies with local and state governments.

Understanding relevant government agencies, programs

As you report on your favorite estuary, a lot will depend on the unique configuration of local, state and federal government agencies whose actions affect it. Here’s what to look for:

  • Municipal and county governments. Local governments have a big effect on what pollution goes (or doesn’t go) into an estuary. Stormwater pollution is affected by zoning and building codes, sewage agency actions, street-cleaning, construction practices and the engineering of runoff.
  • Port authorities. Larger industrial ports or terminals are often organized as something like a “port authority,” with their own funding streams and regulations. How strict their rules are, and how strictly they enforce them, can make a big difference in how much pollution goes into estuarine waters.
  • State economic and environmental agencies. Every state has one or more agencies responsible for protecting the environment, and other agencies responsible for promoting commerce and industry. In some states, these missions overlap, which can lead to conflict.
  • Regional entities. Some of the bigger and better-loved estuaries have evolved their own regional organizations to organize and advocate for them. One good example is the Chesapeake Bay Program, which brings together some 19 federal agencies, 40 state agencies in seven states, 1,800 local governments, 20 academic institutions and 60 private organizations.
  • NOAA coastal zone management. Congress passed the Coastal Zone Management Act back in 1972, when the need to develop energy facilities in coastal areas was colliding with the need to protect coastal environments. Under the federal rubric of the National Oceanic and Atmospheric Administration, each coastal state (there are 34) runs its own program. Some are stronger and more regulatory than others (see California’s Coastal Commission). Once a state has set its own “CZM” plan, federal actions are supposed to be consistent with it.
  • Other NOAA Programs. NOAA operates a number of other programs that affect estuaries — too many to discuss at length here. NOAA’s research vessels sometimes study estuaries. The sub-agency known as NOAA Fisheries is involved with estuaries in many aspects of its fisheries research and management. NOAA also manages the National Estuarine Research Reserve System in partnership with states.
  • Wildlife refuges. The many marshes, wetlands and other resources along the nation’s estuaries are prime fish and wildlife habitat, and many of them have been legally set aside for conservation in the National Wildlife Refuge System, managed under the Interior Department’s U.S. Fish and Wildlife Service, or USFWS. Part of the program focuses on coastal resources.
  • Other federal agencies. Estuaries’ importance is reflected by the fact that several other federal agencies engage with them. The National Park Service manages many estuarine lands and waters — and has its own programs for protecting and interpreting them. The Agriculture Department’s Natural Resources Conservation Service, or NRCS, is also involved in estuary conservation efforts, through things like its Wetlands Reserve Program. The U.S. Army Corps of Engineers conducts a variety of projects, such as dredging for shipping channels, that affect estuaries.
  • Estuary Restoration Act. Passed by Congress in the year 2000, the act aims mainly at projects to restore habitat done in partnership with states and even private groups, with some federal funding. The projects are evaluated by an interagency body called the Estuary Habitat Restoration Council. Agencies involved include NOAA, U.S. Environmental Protection Agency, USFWS, NRCS and the Corps. This law defines estuaries as including the Great Lakes.
  • EPA estuaries program. The EPA’s National Estuary Program was mandated under the Clean Water Act, although it is voluntary rather than regulatory. While there is an umbrella of EPA oversight and funding (EPA is one of the biggest funders of estuary programs), it depends on Congressional appropriations. The Trump administration has proposed defunding many of these programs in its 2018 and 2019 budget proposals, cutting deeply or eliminating EPA funding for estuary programs across the board, including the Chesapeake Bay, Puget Sound, San Francisco Bay and the Great Lakes, while also proposing slashing some NOAA coastal programs (not only the CZM programs, but the Regional Coastal Resiliency grants and Sea Grant). Almost invariably, however, each of the EPA’s 28 estuary programs has intense local popular support and loyal backing from the region’s Congressional delegation. So Congress members trying to protect their districts’ environments (and working through a Congressional Estuary Caucus) have kept the programs going, ignoring the White House and funding them.

Joseph A. Davis is a freelance writer/editor in Washington, D.C. who has been writing about the environment since 1976. He writes SEJournal Online's Issue Backgrounders and TipSheet columns, directs SEJ's WatchDog Project and writes WatchDog Tipsheet and also compiles SEJ's daily news headlines, EJToday.

* From the weekly news magazine SEJournal Online, Vol. 3, No. 17. Content from each new issue of SEJournal Online is available to the public via the SEJournal Online main page. Subscribe to the e-newsletter here. And see past issues of the SEJournal archived here.

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