Estuary Strategy Habitat, Siletz Bay
Photo Credit: DLCD, ODFW

Estuaries occur where freshwater rivers meet the oceanic salty waters, are influenced by tidal flooding, and experience frequent periodic changes in salinity, water levels, sunlight, and oxygen.


Estuaries are a Strategy Habitat within the Coast Range ecoregion and are also discussed within the Oregon Nearshore Strategy.


Estuaries extend inland and upstream from the mouth of a river or bay to the point where the average difference in water level caused by tidal change is 0.2 feet (0.06 meters). Many Oregon estuaries have a large freshwater tidal zone, where water is fresh but water levels fluctuate with the tides. There are 22 large estuaries and many smaller estuaries along the Oregon coast. As a planning tool, the 22 estuaries have been designated as development, conservation, or natural, which define the prominent use or activities in the estuary and specify allowed locations for various uses. Portions of the larger estuaries have been altered through dredging, filling, or diking. Estuaries designated as “conservation status” are in a more natural state. All of Oregon’s estuaries are crucial to the coastal and nearshore ecology and support a diversity of habitats including open channels, tide flats, eelgrass beds, salt marshes, tidal swamps, and freshwater marshes.

Physical Environment:

Oregon’s estuarine habitats can be described using the Coastal and Marine Ecological Classification Standard (CMECS), a federal classification system adopted in 2012 to provide a common framework using a simple, standard format and common terminology. The CMECS classifies the environment into biogeographic and aquatic settings that are differentiated by features influencing the distribution of organisms. Within these systems are four underlying components that describe different aspects of the seascape: water column, geoform, substrate, and biotic. The components can be used to classify a given area depending on the objectives. The goal of using the CMECS is to both enhance scientific understanding and to advance ecosystem-based and place-based resource management.

The Estuarine Aquatic System is composed of both riverine subsystems and the more saline subsystems found lower in the estuary. These are divided where the average salinity during the annual low flow period is less than 0.5 practical salinity units. The species found in the tidal riverine coastal and tidal riverine open water subsystems differ greatly from those found in the more saline coastal and open water subsystems in all of the tidal zones.

Estuaries can also be classified by their geoform components. Geoforms, which are geologic in origin, include sloughs, tidal channels, creeks, deltas, fans, shoreline fans, flats, islands, lagoons, marsh platform, natural levees, and shores. There are also biogenic geoforms, such as burrows and areas of bioturbation. The CMECS also allows the classification of anthropogenic altered areas as geoforms. Such things as shorelines hardened by rip rap (e.g., large rock) structures, artificial aquaculture structures, man-made levees, docks and piers, dredge deposits, dredged and excavated channels, fill areas, and harbors, marinas, and boat ramps are some examples.

Similarly, descriptions of estuarine habitats may include the various substrate components. These components include geologic origin substrates like bedrock, gravel, sand, and mud, for example, as well as anthropogenic substrates, such as the rock of jetties or the construction materials of pilings, and the biogenic substrates, such as large fallen trees.

Biological Community:

This highly complex, productive habitat is critical for many fish and wild­life species, including salmon, crabs, and other shellfish, juvenile marine fish, marine mam­mals, and birds. By some estimates, estuaries support up to three-quarters of all harvested fish species, largely due to the high productivity and diversity of habitats, including those provided by eelgrass beds. Primary production in estuary habitats is among the highest of any on earth, meaning that both the visible and microscopic plants produce a tremendous amount of carbon material (from photosynthesis) that supports the base of the food web. Tidal marshes are particularly productive and produce plant material that, when it dies seasonally, is broken down by microscopic bacteria to serve as food for many organisms, which in turn are eaten by larger ones as they are distributed throughout the estuary with the tides. Tidal swamps provide complex habitat with layered vegetation, including low-growing herbaceous plants, shrubs, and trees; large quantities of above- and below-ground woody debris; deep, sheltered tidal channels; and deep soils rich in organic matter.

Many other fish and wildlife species also use estuaries. Elk herds graze in tidal marshes and shelter in tidal swamps, bears forage in tidal swamps, river otters build their homes here, and rails, snipe, and songbirds nest in the dense vegetation. Estuaries also provide important wintering habitat for waterfowl, including the Black Brant, and migration stopover feeding areas for many shorebirds. Native eelgrass is an important component of an estuary, providing important habitat for several nearshore Strategy Species, including Black Brant, Dungeness crab, black rockfish, copper rockfish, and kelp greenling. Eelgrass is also an important spawning substrate for herring, an important forage fish species.

Conservation Overview

Efforts to conserve healthy estuarine areas and restore degraded habitats will benefit many species, including several commercially important fish and wildlife species. For example, coho salmon, Chinook salmon, and Dungeness crab are Strategy Species that use estuarine habitat for at least part of their life cycle.

Estuarine habitats have been impacted by human development activities, such as urbanization, diking, ditching, and other hydrologic modifications. Tidal wetlands (e.g., salt and fresh water marshes and tidal swamps) have been diked, drained, and converted to pasture. Shrub and forested tidal swamps, once common, have been even more heavily impacted, resulting in substantial habitat loss.

In accordance with state planning laws (Goal 16), local government comprehensive plans and zoning ordinances have been prepared for all of Oregon’s estuaries. Additionally, both estuaries and eelgrass beds are habitat types that have been designated as a Habitat Area of Particular Concern under National Marine Fisheries Service’s (NMFSEssential Fish Habitat regulations for salmon and groundfish species, designations that require federal agencies to consult with the NMFS before actions are taken.

In addition to the Limiting Factors and Recommended Approaches presented here, impacts to species within estuarine habitats can include the removal of animals for harvest or other purposes, which can impact populations; disturbance to various wildlife species including pinnipeds or birds from aircraft, boats, recreation, and research, which may lead to changes in animals’ foraging behavior, abandoning young, or greater susceptibility to predators; and noise pollution, which can impact animal behavior.

Limiting Factors and Recommended Approaches

Limiting Factor: Increasing Development, Land Use Conversion, and Altered or Blocked Tidal Flow

Estuary habitat has been lost to a variety of causes, including: diking, ditching, and drainage; tide gates; inadequate flow through culverts under roads and railroads; industrial and residential development; log storage areas, pilings, docks, or bridge structures; and aquaculture practices that reduce eelgrass beds and disturb winter waterfowl. Estuarine development closer to the ocean can impact habitats as well. For example, building and maintaining jetties, piers, breakwaters, marinas, and navigation channels, including disposal of dredge materials, can alter the habitat and impact nearshore Strategy Species.

Recommended Approach

Continue to provide incentives to protect, conserve, and restore estuaries. Where appropriate, work to restore hydrology to tidal wetlands by removing dikes, filling ditches, and replacing undersized culverts. Continue successful education programs focused on the function and services provided by estuaries. Work with agency partners to support and implement existing land use regulations that preserve and restore habitats. For example, refer to seasonal in water work window for estuaries designed to minimize impacts to out-migrating salmon. Continue to develop and refine “best management practices” for aquaculture. Maintain and restore eelgrass beds as a habitat feature. (KCI: Land Use Changes)

Limiting Factor: Alteration of Freshwater Inputs Into the Estuary

In addition to the restoration of tidal flow discussed above, the amount and timing of freshwater inputs into estuaries are critical in maintaining the hydrological regime that supports the delicate estuarine balance. When either the amount or timing of freshwater input is altered, several results are possible: inundation of floodplains, increased sedimentation, decreased residence time of water (which reduces the filtering benefits of estuaries), altered fish community dynamics, and/or increased stress on juvenile fish, nekton, or other animals. Changes in hydrological regimes can make estuaries prone to invasive species, which compound the problem.

Recommended Approach

Evaluate the potential impacts of water diversions from the estuary (e.g., for agriculture, residential, or industrial purposes) on floodplain dynamics and other functions of estuaries. Prioritize basins for the acquisition of sufficient instream flows.

Limiting Factor: Degraded Water Quality

Water quality in estuaries is degraded by both point and non-point sources of pollution both within the estuary and from its contributing watershed. Runoff from residential, agricultural, and forest land, failing septic systems, animal waste, and storm events can affect water quality. Water temperature can be affected by dredging or sedimentation and stormwater runoff. Oil discharge and spills also affect water quality. Other discharges, such as runoff from boat and ship yards and fish processing operations, can also be a factor. Among other issues, estuaries are susceptible to increased bacterial loads. Low dissolved oxygen levels are often an additional concern. Estuaries are also affected by acidification effects from terrestrial input, which combined with ocean water acidification, can decrease water quality for some marine organisms in estuaries.

Recommended Approach

Continue current efforts to consider impacts on estuarine water quality in land use planning. Support efforts of the Oregon Department of Environmental Quality (DEQ) to assess water quality and develop Total Maximum Daily Loads and water quality management plans where necessary to address issues. Continue coordination to ensure that plans and goals consider impacts to water quality sufficient to protect fish and wildlife in addition to other goals (i.e., recreation). (KCI: Water Quality and Quantity)

Limiting Factor: Invasive Species

Non-native invasive plants and animals can easily disrupt the estuary environment. Invasive plants can alter water circulation and sediment patterns. For example, common cordgrass poses a great threat to Oregon’s estuaries. Common cordgrass has been documented in two Oregon estuaries and is well-established in Washington and California. Where it occurs, it reduces mud flat habitats, disrupts nutrient flows, displaces native plants and animals, alters water circulation, and traps sediments at a greater rate than native plants, thus altering the elevation and the resulting habitats. Three other cordgrass species have invaded the Pacific coast and threaten Oregon’s estuaries. Invasive plants can alter ecological community dynamics, such as competition, predation, or even parasitic relationships with native species. Estuaries are one of the most vulnerable habitats for invasive species due to ship traffic and release of ballast water. Ballast water can also carry invasive animals, algae, protists, and potentially, bacteria. Invasive species can also be introduced into estuaries through aquaculture, recreational or commercial boating, or the aquarium trade. Examples of non-native invasive animals found in Oregon estuaries include: the parasitic Griffen’s isopod which has been linked to declines of native blue mud shrimp populations, the Japanese oysterdrill, the New Zealand mudsnail, the purple varnish clam, and a colonial tunicate.

Recommended Approach

Emphasize prevention, risk assessment, early detection, and quick control to prevent new invasive species from becoming fully established. Control key invasive plants using site-appropriate tools, such as hand-pulling, covering with geotextile cloth, repeated mowing, flooding, and/or herbicides focusing on spot treatment. Monitor estuaries for potential invasive species, and use site-appropriate methods to control newly-established species for which management can be most effective. Work with partners to implement existing ballast water regulations. Develop methods to treat ballast water. Work with partners to limit the spread of invasive species that are established. Allow increased harvest of species suitable for human consumption such as purple varnish clams. (KCI: Invasive Species)

Limiting Factor: Coordination of Management

Many jurisdictions and agencies have management authority and interest in estuaries, which can make management more complex and difficult. In Oregon, 22 cities, 7 counties, 13 port districts, many state agencies (e.g., Department of State Lands, Oregon Water Resources Department, Oregon Department of Land Conservation and Development, DEQ, Oregon Department of Agriculture (ODA), ODFW, Oregon Parks and Recreation Department) have planning and management responsibilities for estuaries as does the federal government. Many organizations have interests in estuaries.

Recommended Approach

Coordination among agencies is a high priority. Because estuarine issues are complex, clear identification and communication of conservation opportunities, goals, and threats should precede management actions, ensuring that all interests are considered and coordinated.

Limiting Factor: Loss of Habitat Complexity

Habitat complexity provides refugia for estuarine fish and wildlife. Complex habitat supports diverse ecological communities, contributing to resiliency to climate change impacts. Removal or loss of large downed trees reduces habitat complexity, insect production, and food and cover for juvenile salmonids. Disconnection from the floodplain interrupts the natural transition zones between the aquatic, intertidal, and upland ecosystems. Dredging, ditching, channelization, and filling in estuaries alters marine and freshwater inputs and reduces habitat function. In-water (e.g., pilings, jetties, seawalls) or overwater (e.g., mooring buoys, floating docks) structures can reduce habitat complexity, as can bayside development that extends into intertidal areas. Natural factors can also reduce habitat complexity, such as damage or movement caused by seasonal runoff or significant storm events, especially where the estuary has already been compromised and floodplains have been lost.

Recommended Approach

Assure that permit application reviews consider alternative sites and practices to reduce and minimize impacts, and provide full mitigation. Encourage and participate in cooperative efforts and incentives to promote habitat complexity in estuaries. Prioritize conservation and restoration efforts to restore floodplain connectivity, tidal marshes, and swamps and to conserve eelgrass. Increase outreach and education about the importance of habitat complexity.

Limiting Factor: Climate Change

Climate change may impact estuaries in several major ways: loss of wetlands due to sea level rise, alteration of hydrology, increases in erosion and salinity, changes in storm patterns, and ocean acidification. The effects of sea level rise are being modeled in Oregon’s estuaries, incorporating tectonic uplift, different levels of predicted sea level changes, and information on sediment inflow. The goal is to identify which estuarine areas are the most susceptible and where future marshes are likely to be to help restoration specialists and planners define desired future conditions and actions. Additional information is needed to understand the effects of climate change (including storm surge impacts and sediment movement patterns) on species with a variety of life stages in estuaries. Ocean acidification and the impact of anoxic (hypoxia) conditions in estuarine and nearshore areas are also of concern. Additional information is needed to determine what adaptation measures can be taken.

Recommended Approach

Use emerging models of future sea level rise and changing salinity regimes to inform conservation actions in estuaries. Work with property owners, land use planners, and restoration practitioners to focus attention on vulnerable areas. Support efforts to restore natural processes of tidal exchange and sediment deposition, which will enable tidal wetlands to maintain their elevation relative to rising sea levels. Support efforts to re-connect floodplains to adjacent uplands by removing barriers, placement of large woody debris, and planting of riparian areas. Conserve areas that will become new marshes with sea level rise. Inform communities about climate change impacts and support community preparedness. (KCI: Climate Change, Climate Change and Oregon's Nearshore Open Water Habitat)

Limiting Factor: Oil Spills

Oil (and other hazardous waste) spills are of concern in estuaries. If a spill occurs, oil accumulation can have lasting impacts in estuaries.

Recommended Approach

Review and update oil spill contingency plans based on new estuary maps and climate change considerations. Work with Oregon Department of Geology and Mineral Industries, DEQ, and local emergency officials to identify hazardous material use and storage sites in high risk areas and seek ways to minimize these risks.

Resources for more information