Where River Meets Sea Mapping the resilience of wetlands

43.2959° N, 124.3347° W



"A transition zone between the freshwater of creeks and rivers and the saltwater of the ocean."

South Slough Reserve, Charleston OR

The South Slough Estuarine Research Reserve in Charleston, Oregon, was the first of its kind designated in the U.S. in 1972. The National Estuarine Research Reserve System includes 28 other estuaries around the coastal U.S., each designated for long-term research, wetland preservation and education purposes.

Fossil Point

Just north of the turbid, tidal waters of the South Slough, a tall, white-haired man picks his way along a rocky shoreline. With deft steps, he navigates around saltwater pooling in crevasses, and treads nimbly across fine layers of slippery algae and clumps of washed-up sea palm.

He stops and bends over to the ground, running his fingers along the outline of a fossilized scallop shell, its edges etched in the surface of the brown sedimentary rock. It’s a piece of visible history dating from the Miocene epoch, embedded into the dimension of the landscape.

A little further down the shore, he points at what looks like a small protrusion of curving rock, rounded smooth by waves.

“Do you see this? It’s not a rock. This is a fossilized whale bone,” he says. “It looks like a vertebra.”

He pauses for a moment to look across the water toward the thin finger of the inner jetty at Charleston, Oregon. It stretches across the southern section of Coos Bay, protecting Charleston’s marina from the onslaught of winter storm waves; storms which have occurred with more intensity in recent years.

Since visiting the area as a college student in 1975, marine biologist Mike Graybill has walked the shores along the edge of the Coos Bay Estuary at Fossil Point.

Just inside the dredged channel sits a wrecked salmon fishing boat, its hull slipping backwards into the silver-grey waters.

“If that's a metaphor for an entire fishery to be on the rocks, I can't think of a better one,” he says.

He watched the salmon fishing and logging industries flourish in the 1970s during their heyday in Charleston, and watched them recede from the town like the tides of the bay over the last 30 years.

For 28 of those years, Graybill worked as the manager of the South Slough Estuarine Research Reserve, the wild southern fork of the Coos Bay Estuary, just a few miles south of Fossil Point.

“The thing that kept me awake at night before the South Slough management commision meetings was not so much related to shrimp and clams, but it was the incredible burden of responsibility that was granted to me to manage this incredible natural place on behalf of all the people.”

Oscillating Waters

Estuaries are damp, muddy places.

“I like to think of an estuary as a hole in the continent where the water drains out,” said Graybill.

They are also one of the biomes most essential to human civilization, and estuaries play key roles in the processes of the natural world.

A biome: A broader term than habitat, a biome is a major community of plants, animals and other organisms adapted to a specific environment, such as a wetland or desert.

More than 140 miles of freshwater streams drain into the South Slough estuary, mixing in a ceaseless cycle with the saltwater tides of the Pacific Ocean.

The South Slough is inundated with seawater twice a day in what’s called a semidiurnal tide. The murky mixture of fresh water and sea water deposits layers of sand, silt and mud miles into its tidal channels. South Slough has tidal mudflats and sandflats, salt marshes, and freshwater marshes at its southern reach. The marshes act like a sieve, filtering sediments from the water and absorbing pollutants.

A spectrum of river and sea-dwelling plants and animals reside in the brackish, ever-changing waters. The diverse conditions of the estuary create habitat vital for shellfish, fish, salmon, birds, river otters, beavers, elk and humans.

Elk make their beds in the long marsh grasses.

“Civilization that occurs here today would not be possible without the sheltered waters of the harbor that are provided by this estuary,” said Graybill. “Western civilization would not exist without the current relationship that it has with maritime activities.”

Twenty-two of the world’s largest cities are built on estuaries, according to the National Oceanic and Atmospheric Administration.

Estuaries are often named as bays, lagoons, sounds or sloughs. The Coos Bay estuary is the second-largest in Oregon, and branches into the South Slough at its southern point.

In the lower level marshes, high tides create small tidal creeks into the marshlands making it easier for crabs and fish to access the marshes.

It is a coastal plains estuary; the sea floods the valley mouth where the watershed flows into the ocean.

In a watershed, creeks and rivers coalesce along the same slope of land or valley and drain to a nearby place. The watershed that drains into the South Slough is about 600 square miles, said Graybill.

Six year-round creeks and about 20 seasonal creeks flow into the slough. The largest is Winchester Creek.

Part of the mission of the reserve is preserving the natural beauty of the estuary for the enjoyment of visitors and future generations.

Because of the constant flow of salt and fresh water, salinity levels in the slough fluctuate, varying by season and by tide.

“Estuary conditions really change depending on the nature and delivery of water into the estuary,” said Graybill. “Rivers that feed this estuary fluctuate very dramatically on a seasonal basis.”

From the drier summer months to stormy winters, creek water flow changes by a factor of 60, he said. In the summer, less fresh water drains into the estuary and the salinity from seawater is stronger.

Salinity also changes like a gradient in the estuary; near its mouth, the slough waters have ocean-like characteristics.

“As you move up into an estuary, the signal of that ocean tends to diminish because the signal of the river begins to emerge,” said Graybill. “If you're a salmon, if you're a crab, if you're anything that lives in the water that's sensitive to that, you're going to know about that signal.”

Just as salinity levels rise and fall, so does the estuary’s acidity, or PH. But instead of the tides, it changes with the rising and setting of the sun. Chlorophyll producing plants like eelgrass and tiny organisms like phytoplankton use energy from sunlight during the day. They generate oxygen while absorbing water-acidifying carbon dioxide in a process called photosynthesis. At night, these photosynthetic processes stop, the water acidity rises, and dissolved oxygen drops, said Graybill.

“Estuaries are dynamic places. The tides come, the tides go. The seasons come, the seasons go. Huge changes happen within each of those periodic cycles,” he said.

Two miles up Winchester’s tidal channel, the creek waters swell to a 10-meter width during high tide. Withstanding the daily shifts in salinity and tide, barnacles cling to the large wood pilings lining the creek’s curves. Young Coho salmon swim the estuary waters, acclimating to oceanic conditions. Standing as still as statues, great blue herons linger in marsh meadows of slough sedge and reed canarygrass, eyeing the silt for young crabs and small fish.

Beds of marine eelgrass undulate in the tides, providing shelter for species of shellfish and fish, like juvenile Dungeness crab and salmon. Small creatures hide from the heron’s watchful eyes among the meadows of eelgrass and marsh plants.

The estuary is at once a balance of resilience and fragility, an ever-cycling biome of riverine, marine and terrestrial life.

Large estuaries like the Coos provide a bigger diversity of environments for plant and animal life to flourish. Smaller estuaries have fewer habitats with less variety for organisms to live in.

Purple martins make their homes in the South Slough wetlands, nesting inside boxes provided by the reserve as part of an effort to increase bird habitat.

“Fewer species live in smaller estuaries,” said Graybill. “The bigger estuary has a greater variety of places to live and you find a larger variety of organisms.”

That’s why, he says, the South Slough was the perfect place to designate as a research reserve.

Extinctions are more frequent in small estuaries because of the fluctuating environmental conditions, which often exceed the threshold that some organisms can withstand, according to Graybill.

“Some people ask why the South Slough was designated in a large industrial estuary where there’s all kinds of human activity,” said Graybill. “Well, I could make the argument that it’s perhaps the very best place in Oregon to designate a site for long-term research and education, because it’s one of those species-rich estuaries that may actually provide propagules that resupply smaller estuaries.”

The South Slough Estuarine Research Reserve doesn’t encompass the entire South Slough; it is a 5,900-acre natural area beginning just south of the estuary mouth, where the town of Charleston hugs the curve of Coos Bay.

At high tide, the Coos Bay estuary swells to 10,000 acres. But when it was still pristine, it grew to encompass about 20,000, he said.

“We've changed the shoreline of the estuary and removed about 90 percent of the fringing tidally-influenced marshes by diking and agricultural practices,” said Graybill. “So, this estuary is functioning as a very rich place, but it's greatly transformed by past human activities.”

Estuaries provide the perfect place for human harbors, allowing industries dependent on shipping and fishing to flourish along with the plant and animal life.

“We also depend on estuaries as a place to nurture us. They’re a source of rich food. They’re an important part of cultural economies for all people,” said Graybill. “The fisheries that are here depend on the richness of the coastal area in this vicinity. The same has been the case for the entire history of human civilization in this place and anywhere on the planet.”

The Handshake

Graybill arrived in 1975 for an undergraduate college summer session at the Oregon Institute of Marine Biology (OIMB), the University of Oregon’s graduate and research campus.

“I was overwhelmed at the richness of the natural world that’s in the vicinity of Charleston,” said Graybill.

It was just one year after the South Slough had been designated as the first estuarine reserve in the nation, to be managed in partnership under the auspices of the National Oceanic and Atmospheric Administration (NOAA) and the state.

Graybill says the designation of the South Slough in 1974 acted like a “handshake” between Oregon and the federal government.

“It’s a very simple law. It’s two pages long. But it sets out the purpose of the reserves, which is to be used for long-term research and education, and it sets out how it should be managed.”

The South Slough was the first implementation of the 1972 federal Coastal Zone Management Act. The act recognized that estuarine regions like the South Slough were vital to fisheries and economic activities, according to Graybill.

“The intensification of human development on the shorelines of estuaries, these places that form where rivers meet the sea, was going to accelerate through the coming years,” said Graybill. “There was a calling by congress to better understand the role that estuaries play in fisheries, in our economy and in all the other uses that human civilization depends on them for.”

Graybill says the reserve is protected from human activities and uses that would alter the dynamic processes of the estuary ecosystem, within and beyond its boundaries.

A commission appointed by the governor of Oregon oversees the South Slough estuary management, and includes representatives from local interests, including the port, community and research institutions. [EG4]

“Many of the people who were my mentors at OIMB were involved in the development of the proposal to designate the South Slough as a special protected area,” he said. “There was a great deal of interest and enthusiasm about this newly created place, what it would be used for and how to get people involved.”

Mike Graybill shows Science and Memory students around Fossil Point.

There was also some controversy, according to Graybill. Because the cities of Coos Bay and North Bend are coastal and inextricably linked to the estuary by the waters of the bay, the cities had to develop comprehensive land use plans and Coos County developed an estuary management plan.

“In 1974 and 75, that was a very controversial and newly instituted practice and, needless to say, there were a lot of skeptics and a fair few opponents,” said Graybill.

Now, the South Slough serves as a living laboratory to a slew of scientists and researchers. It’s part of a network of 28 other reserves around the coastal U.S., the National Estuarine Research Reserve System.

The system preserves estuaries that are representative of the many different types, and designates them for research and education, said Graybill. Its mission is to improve how humans understand and interact with the areas.

The types of wetlands in the reserve system vary, from the mangrove swamps of Florida to the glacier-carved fjords of the Puget Sound.

A Continental Signal

“The natural world and places that are managed to emphasize the natural dynamics of the ecosystem will be the place where the signal of climate change can be measured as much as possible in the absence of other disturbances and activities,” said Graybill

The reserve system has created a web of data, constantly checking the pulse of wetland biomes.

“There's a camera or a recording device on the landscape at the scale of the continent now, that can measure large-scale signals like hurricanes, oil spills, sea level rise and climate change,” said Graybill.

In what they call the System Wide Monitoring Program (SWMP), reserve biologists are partaking in a national data collection system. They’re monitoring short and long-term changes in water quality, species diversity and characteristics of the marshes and lands in the reserves.

(Left Photo) Part of the System-Wide Monitoring Program swamp stations, a water quality monitoring device called a sonde sits underneath the waters of Winchester Creek. In 15-minute intervals, it measures the pH, or acidity of water, total alkalinity, carbon dioxide and dissolved organic carbon, turbidity, salinity and water temperature. (Right Photo) A water quality sonde like this blue one takes real-time measurements in the South Slough marshes.

In that data, researchers are looking for signals – the signals of climate change.

Climate change is an accelerated warming of the earth’s atmosphere. Over the last 200 years, the burning of fossil fuels like gasoline and oil released vast amounts of stored carbon into the atmosphere.

“We’ve got highly elevated levels – unprecedented elevated levels – of carbon dioxide in the atmosphere in human history,” said Graybill.

When sunlight enters the atmosphere, it becomes infrared light, which warms the earth. It leaves the atmosphere slowly because it’s trapped by greenhouse gasses like carbon dioxide. The more greenhouse gasses in the atmosphere, the warmer the earth becomes.

Certain biomes like forests, marshes, and the ocean help balance warming by pulling carbon out of the atmosphere and storing it through photosynthesis and a process called carbon sequestration. Carbon is one of the major components of organic life on the planet.

In the past, the oceans have absorbed enough carbon dioxide to keep the earth from warming dramatically, said Graybill. The ocean is absorbing about half, but it’s not enough.

One of the most measurable effects of climate change is the increased acidity of the ocean, and it’s been studied with the SWMP.

“It's an important issue,” said Graybill. “It's particularly manifesting itself on the Oregon coast because of the oceanographic conditions that exist here.”

When carbon dioxide in the atmosphere meets the ocean, it dissolves in the water. The more carbon dioxide added to the water, the more acidic it becomes.

“If you think of Pepsi Cola or carbonated soft drinks, the carbonation in soft drinks is the result of the injection of carbon dioxide into the water,” said Graybill. “So, on a much more mellow scale, the same thing is happening in the ocean.”

For shellfish, crabs and tiny foraminifera in the estuary or ocean, and especially as larval young, an acidic ocean makes life conditions difficult.

Creatures like crabs pull calcium from estuary waters to grow their shells. When they outgrow them, they molt, leaving behind the empty figures of their former exoskeletons in the marsh grasses.

“Think of a clam; it grabs calcium out of the water and makes its shell with that. That’s a bit of chemistry that the animal undertakes,” said Graybill. “When the PH of the ocean is changed, it’s harder to do that chemistry project.”

Marine biologist Ali Helms is the estuarine monitoring coordinator at the South Slough Reserve. She monitors water quality for the SWMP at six stations set up along the salinity gradient throughout the reserve.

Helms and the others working on the SWMP are trying to tweeze out how increased ocean acidification is affecting the estuary, said Graybill. But this isn’t a simple task in an ever-fluctuating estuary; scientists need huge amounts of long-term data before real climate change signals can be isolated.

“PH in the estuary is really complicated by tides, currents; lots of things like plant respiration and production influence PH,” said Helms. “It's not a simple measurement.”

A lower PH measurement means the water is more acidic, and vice-versa.

“Water temperature in our estuary is definitely increasing,” said Helms. “We've seen a lot of changes in these physical water parameters that could eventually drive or influence what's happening with the nutrients.”

The PH trends Helms did find were surprising. At first, as the ocean became more acidic, Helms’ data showed the estuary in a reverse trend, decreasing in acidity. After deploying an oceanographic instrument called a sonde to a site the middle of the estuary, Helms’ data showed that trend switch in 2016.

“We're still collecting data. We don't really know exactly what's going on, but the trend changed,” said Helms. “So now we're looking at the patterns. We're comparing the sonde PH with both high resolution PH as well as with the carbon dioxide. Eventually we’ll be able to answer questions about the carbon system itself.”

Meet the Scientists

Marine biologist Ali Helms is the estuarine monitoring coordinator at the South Slough.
Marine biologist Jenni Schmitt is the watershed monitoring coordinator at the South Slough.
College student Kerrigan Buck is an intern at the South Slough.

Inundation and a Rising Tide

One of the biggest climate change threats to estuaries is sea level rise. But marshes can temper the effects if they are building enough new sediment to keep pace with the rising tides, a process called sediment accretion.

Jenni Schmitt stands in knee-high rubber boots in the tall marsh grasses, water pooling up to her ankles. She’s holding a long, thin silver pole, taller than her head – a Russian peat borer. It is hollow and pointed on the bottom. Using two hands, she slams it into the soggy ground with her body weight, until it slides through the tangled root system of marsh plants and into the sediment below. When Schmitt pulls it up, it is holding a cylindrical sampling of earth in its hollow point.

Schmitt is the watershed monitoring coordinator at the reserve. She’s tracking levels of sediment accretion in the estuary as part of the Sentinel Site Program, a research initiative within the national reserve system to better understand how estuaries are vulnerable to climate change.

“We’re trying to understand how our marshes and our eelgrass beds and our forested swamps are going to be changing as the climate changes,” said Schmitt. “As ocean patterns are changing, as sea levels rise, how is that all going to affect our marsh communities?”

The sentinel site program monitors marsh elevation, tidal range, coverage of the plant communities and the salinity of groundwater.

Marshes that are low will be more susceptible to sea level rise than marsh plants at higher levels, said Schmitt.

“Having a large tidal range makes you more resilient to sea level rise,” said Helms. “Having a low tidal range makes you more susceptible.”

In Schmitt’s and Helms’ data collections, they are looking for trends that will point out vulnerabilities in the South Slough’s marshes.

The reserve participated in a 2016 tidal marsh resilience to sea level rise study among the national reserves, or the MARS study.

This study created measurable guidelines, a comparative index that other researchers can use to evaluate estuaries and sea level rise.

“If you have elevations of plants or plant community data, if you have a tide station – which a lot of people do – you can plug in your numbers and calculate what your vulnerability would be at a different site,” said Helms.

Unlike other study participants, the South Slough researchers only had four years of data for the MARS study, which isn’t enough to show a good long-term trend.

“What came out of this study was that there wasn’t a single metric. They all kind of interplay together,” said Helms. “You need to look at the integrated response through all these different variables. That was the take-home message.”

The reserve’s NOAA tide gauge station calculates long-term sea level rise, said Helms, and the current rate is 1.12 millimeters per year.

It might seem like a small amount, she said, but the effects accumulate, and each year the rate increases.

“It’s about the long-term effects of that rate, what that’s going to do to marshes, because they’re going to be underwater eventually,” said Helms. “We’re not accreting a lot of sediments, which would help the marsh keep pace with sea level rise.”

Like intermittent sponges along a rocky coastline, Oregon’s marshes soak up flood waters from storms and high tides, mitigating damage to properties.

“Flooding is a huge hazard on the coast, and flooding is happening more and more often, because as the climate is changing, we have stormier winters with higher precipitation,” said Schmitt. “Marshes are really good at dampening the effects of flooding.”

But sponges can only hold so much before they are submerged. As tidal marshes absorb the rising sea, the likelihood of flooding during winter storms rises, too.

The Resilience of Rhizomes and the Case of the Disappearing Eelgrass

Plants shape the landscape of a marsh. Their roots create dimension and structure. Long stems trap silt suspended in the water, improving the water’s turbidity. When plant bodies decompose, they accumulate in layers of rich loamy detritus on the marsh floor. Eelgrass beds create shelter beneath the waters of tidal channels for estuarine life.

Rhizome: A continuously growing horizontal underground stem that can produce shoots and roots.

Meter-long pieces of it float through Winchester Creek during high tides. King tides sweep the creek waters so high that the strands become tethered to low hanging branches. In some places, dried-up pieces of it decorates the riparian trees like withering Christmas streamers, rustling and lilting in the breeze above the creek.

In northern parts of the Coos Bay estuary, eelgrass beds are thriving. But in parts of the South Slough, they are vanishing.

Helms has over a decade of data from four eelgrass monitoring sites on the estuary. At Valino Island, near the center of the reserve, eelgrass was growing in abundance. She holds a photo of the site from 2002, filled with eelgrass just beneath the water’s surface.

“At the same site, it’s barren,” says Helms. “There’s a small patch of eelgrass, there’s lots of macroalgae and the rest is just intertidal mudflat. Look at the stark difference. Eelgrass is gone.”

Danger Point, the eelgrass site furthest south on the reserve, used to have 90 percent coverage in eelgrass in the areas she surveyed. Now there is none.

As a scientist, Helms isn’t going to guess why, but she has several hypotheses to research. She knows with certainty that in the fall of 2016, something, or a combination of stressful conditions, caused the eelgrass to disappear.

“It’s very localized,” said Helms. She’s checked with other eelgrass sites in the Coos Bay region, and no other places are experiencing the same population decline.

She’s working with the Oregon Department of Fish and Wildlife and local conservation and research groups to form an eelgrass advisory committee.

Helms said a graduate student from OIMB is researching eelgrass wasting disease and has positively identified it in the estuary. But estuaries with the disease in Washington have full-density beds of eelgrass; it doesn’t decimate populations up there. It’s probably not the reason for this drastic decline, she said.

An intern at the reserve is piecing together sets of water quality and turbidity data, looking for correlations with the decline. An increase in turbidity could make it difficult for photosynthetic eelgrass to thrive, because it needs light. And decreasing dissolved oxygen could have affected it, too.

Helms said the most difficult hypothesis to research is the possible effects of herbicide applications the Department of Forestry uses in the watershed, because the herbicide could run down the watershed into the estuary.

Helms is proceeding with caution – she doesn’t want to draw any conclusions before more data is explored and research is done.

“If we want to do any recovery projects, we need more information about what’s happening,” said Helms.

Fish and Chips

Since the end of the ice age, the South Slough’s shores have been inhabited by humans. Long before its forests were logged, its marshes diked for farm and pasture, and the mouth of the estuary dredged for a shipping lane, the Miluk lived and fished on its shores.

European-American settlers brought an extractive economy to Coos Bay in the 1850s, centered on logging and fishing. It continued into an intensification of economic development that was not sustainable, said Graybill.

“Coho salmon was one of the most important commercial salmon fisheries in our harbor. There has not been a commercial salmon fishery for perhaps the last 15 years in this estuary,” says Graybill.

He tells a similar story about the timber industry.

“We built a timber economy that was scaled larger than trees could grow,” he said. “We’ve conducted land use practices that have impacted fisheries; we’ve built hydroelectric dams.”

Weyerhaeuser, the logging company, exhausted the timber supply in the Millicoma forest, he said.

“We’ve run out of big logs,” said Graybill.

He recalled a story of an afternoon in Coos Bay at lunchtime, when the mill gave sudden notice of its closure and hundreds of people were left out of work.

“So, the economy in this community has gone through some fairly serious ups and downs. It's largely been based on an extractive resource economy – fish and chips,” said Graybill.

Coos Bay is still one of the largest wood chip exporting ports in the world.

But Graybill thinks the community should search for a sustainable answer to its economic downturn – and says sustainability is a concept measured in centuries, not decades.

“We will still have forests on the coast a century from now. They will still be a valuable resource for us to use. We may not be able to use them and derive the intensity of economic value that we did when we first entered the forest and mined into its history,” said Graybill.

Scientists like Graybill and researchers at the South Slough are searching for ways to preserve and protect the estuary from the most dire consequences of climate change.

But recent winter storms surge with more ferocity, tides are creeping higher, and ocean waters have become more acidic.

“I can’t think of a community that’s not facing the consequences of climate change,” said Graybill. “Will this community survive the consequences of climate change? I’d ask, ‘Well, what choice do any communities have?’”


Words by Emily Goodykoontz

Designed by Denzell Gallegos

Photos by Noah Andrews, Denzell Gallegos and Jessica Smith

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