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Where the river meets the ocean—estuaries are a point of intersection, a mixing. They are ecologically unique, biodiverse, and incredibly productive. Estuaries are safe havens for many species. As borderlands, they function as a barrier that protects the coastline from storms. They are also beautiful places to visit and explore. In short, estuaries matter.

Estuaries are also relatively rare ecosystems—heavily impacted by human development. As dynamic as these places are, they are sensitive to change in a changing world. To better understand these changes, the National Estuarine Research Reserve (NERR) system was established in 1972 as part of the Coastal Zone Management Act (CZMA). Now a network of 30 reserves along the United States Coastline is protected for long-term research, education, and stewardship.

The South Slough NERR near Coos Bay is Oregon’s only estuarine reserve. With nearly 7,000 acres of natural areas, including upland forests, streams, wetland marshes, islands, sand, and mudflats, South Slough offers a wide array of habitats suitable for study and exploration. Alice Yeates, stewardship coordinator, along with Jeanne Standley, retired BLM botanist and board member for the Friends of South Slough, took me on a journey through the estuarine reserve to discover some of these habitats for myself.

The Hike

• Trailhead: South Slough Trailhead
• Distance: 3.4 miles
• Elevation Gain: approximately 350 feet
• Details: Ample parking at trailhead. Visitor Center at trailhead is open every Tuesday – Saturday, 10 a.m. – 4 p.m. Public bathrooms are available Monday – Saturday, 8 a.m. – 4 p.m.

Upland Forest

Alice, Jeanne, and I started our adventure at the visitor center, before quickly taking off onto the Ten-minute Trail, and then onto the North Creek Trail. Immediately, we found ourselves hiking downhill into a mixed-Sitka spruce/Douglas-fir Forest typical of much of Oregon’s coast range. Sword fern, huckleberry, and salal made up the shrub layer, and western hemlock, the lower canopy.

In addition, Port-Orford-cedar—with its scaley, evergreen branches drooping across the trail—joined the mix. I was excited to see the tree and look for the tiny white Xs on the underside of its leaves because, though not necessarily rare, Port-Orford-cedar doesn’t grow naturally in the Willamette Valley where I live. 

“It has a really limited range,” Alice shared, growing only in the southern coast range of Oregon into the northern end of California. It is a local endemic. “We are near its northern extent,” she told me.

Resistant

Unfortunately, many of the Port-Orford-cedars we saw on the trail had orange-colored leaves, especially at the tips of their long branches—a sure sign of illness.

“A lot of them are dying from a root rot disease,” Alice offered.

Jeanne went on to explain how the disease is caused by a non-native Phytophthora fungus—Phytophthora lateralis, to be more specific.

Though new to me, Phytophthora lateralis has been around for at least 25 years—infecting Oregon’s populations of Port-Orford-cedar trees at an alarming rate. The disease is passed between trees in moist conditions, Jeannie told me, with roadway trees seeming to be most affected.

“Phytophthora fungi are responsible for many root diseases, like sudden oak death. And the disease that caused the Irish potato famine is a phytophthora,” said Jeanne. Clearly, some Phytophthora species are seriously problematic.

Fortunately, genetic resistance has been identified in individual trees, and selective breeding programs for Port-Orford-cedar are underway. South Slough is involved in one such program and has been planting resistant trees in place of those that are dying. Several of these trees can be seen on the ten-minute trail—the future of the upland forest.

Getting Wild

We continued downhill, crossing several numbered bridges, and losing elevation rapidly. Salmonberry shrubs proliferated in the drainages, along with elderberry, while evergreen huckleberry grew tucked into the shaded understory.

Bird song filled the air as we hiked, and a rough-skinned newt pattered across the trail.

“We called them water dogs when I was a kid,” exclaimed Jeanne, referring to the newt, as we tip-toed around it.

I asked Alice and Jeanne what other wildlife they have encountered in the reserve.

Racoon, skunk, weasel, river otter, beaver, elk, and deer were all mentioned. And birds.

“There is a lot of bird watching in this area,” said Jeanne.

Take Flight

“There is an interesting story about the Purple Martin,” Alice chimed in.

Purple martin are large swallows with beautiful, sometimes iridescent, bluish-purple plumage.  You can often see them flying rapidly high above the water with their tapered, aerodynamic wings—catching insects in flight.

In the past, purple martin would nest in forested areas, in the cavities of dead standing trees, like those created by woodpeckers. However, as humans have encroached on purple martin habitat, things changed. Now, most purple martin populations use nest boxes or other human-made structures for their nests.

At South Slough, this is also the case, with pilings in the estuary as the primary source of nesting location. The problem is that many of these pilings are now decaying to the point they are not useable. In addition, other purple martin forest habitat needs have also been reduced over time. The result? Population decline.

“They used to be a larger population…but they lost their nesting space,” Alice remarked. “The purple martin were pretty much gone 30 years ago.”

Fortunately, Audubon volunteers have since put in more nest boxes in new locations, including the North Spit.

“They need open water in order to compete against other species,” Alice explained, and “they like dune habitat.”

Forest restoration is also underway to improve the habitat for purple martin, among other reasons, at South Slough. Purple martins need open space to be successful. 

“We recently created a gap in the forest,” said Alice, “girdled trees and installed nesting boxes” near the visitor center. In addition, other forest locations, like near Wasson Creek, have been thinned and more gaps put in.

“The hope is purple martin will use these spaces,” said Alice—and that their populations will soar, like a bird in flight.

Swamped

The trail continued down through the forest, leveling off as we neared a swampy bottomland flooded by North Creek. Down logs lay across the waterway. Skinny stemmed alder trees grew along the mucky edges. The yellow flowers of skunk cabbage peered out from the green-colored waters. You could just make out the sandy bottom where the water flowed clear through a narrow channel. We were nearing the estuary.

Looking out on the flooded forest, reminded Alice of another ecosystem found in the refuge, but only in small quantity—the Sitka spruce swamp.

“The spruce forests around the estuary are critically important for carbon storage,” said Jeanne.

Sitka spruce swamps store more carbon per unit area than most places on the planet. In addition, they provide important habitat for salmonid species.

However, since human settlement, almost all (95% by some estimates) have been lost. “It is easy to cut trees down in swamp areas and rivers,” Alice suggested, “easy to fell the tree and transport it.”

Now, the primary threat to this critical habitat is saltwater intrusion. Though Sitka spruce can tolerate some salt, too much can be problematic for the forest.

“And with climate change, we are expecting saltwater intrusion,” Alice stated with solemnity.

The Wasson Creek restoration is an attempt to expand the Sitka spruce swamp. Most Sitka spruce trees get their start on nurse logs and can grow quickly from there. So, to encourage their growth, a lot of down wood is left on the ground resulting in the formation of hummocks—the perfect nursery for spruce trees.

It’s Not Complex

We continued along past the creek and through a dark, dense area of forest—thick with trees and not much else, other than a scattering of sticks and a few small shrubs.

“Look into the forest here,” said Alice, directing her gaze at the skinny trees. “They were planted really close together.”

The trees grew so close to each other that their narrow crowns were touching. Alice pointed to the lack of understory shrubs below—a sign that not enough light was hitting the forest floor.  It was clear that competition for resources was high.

Dense forests like this one, Alice explained, grow tall and straight trees—good for timber production, but not good for wildlife.

“Some of our healthy forests have more of the sword ferns,” Alice remarked. Looking around, nary a sword fern could be found.

Wildlife do best in forests that are complex, Alice explained, with a variety of sizes and ages of trees, as well as ground cover and understory to provide shelter and food.

Unfortunately, almost all the forest at South Slough has been logged and regenerated at one time or another. The result is a lot of high-density, low-complexity forests.

Fortunately, Alice and her team are slowly working to return complexity to the forest through thinning and selectively cutting. As well as adding biodiversity, by planting disease-resistant, less common, and culturally important species, like the western redcedar.

Complexity isn’t complicated, but it takes a long time to establish naturally. According to Alice, there are only a few remnants of old-growth forest remaining in the reserve. Restoration is a way of speeding up the process to recreate, to an extent, what was lost.

Estuary

We continued through the forest under a low arc of big leaf rhododendron, before reaching a large wooden bridge that stretched across a shallow stream—ah, the estuary.

It was low tide when we made it down to the estuary. Ribbony impressions in the thick mud meandered in the tidal channels. Light from the overcast sky glinted off the thin watery surfaces of each mud slick. Marsh flats of brown grass weaved through and around the edges of the slough. 

“In a few months it will be very green,” said Jeanne as we stepped onto the long bridge. We passed by evergreen huckleberry just beginning to flower.

After crossing the bridge, we took the Slough Side Trail for a better view out onto the estuary. The trail led out onto a narrow peninsula with patches of grass and a couple of trees coated with lichen.  Canada geese flew over our head—honking as they passed.

You could see some rotting pilings sticking out of an adjacent strip of land.

“This is where the nest boxes were,” remarked Alice.

Alice pointed out some of the features of the area, including Long Island and Valino Island set further back in the distance.

“Winchester Creek is the main freshwater source in South Slough,” Alice shared, along with some smaller tributaries, including those that feed the second arm of the slough.

Then, of course, are the tides.

Changing tides

One of the best ways to experience the estuary, Alice suggested as we made our way back onto the main trail system, was to go on a paddle tour and ride the tide.

One of the most important features of an estuary is its tides. In fact, estuaries are often classified by the degree of mixing of saltwater with freshwater in the estuarian system. This is important, as different organisms that live in the estuary have different tolerances for salinity, or how much salt is dissolved in water. Increased salinity also reduces the amount of oxygen dissolved in the water that aquatic organisms require to breathe. Again, different species have different levels of tolerance.

I asked Alice if she was worried about the state of the tides at South Slough. How would climate change impact estuarian systems?

“We are doing a lot of research and monitoring,” she replied. South Slough is part of a sentinel site program to monitor climate change impacts on estuarian systems. 

“We monitor our eelgrass beds… marsh habitat… track changes in elevation… and plant communities,” Alice went on. All in an effort to better understand how species and habitats are responding to climate change.

Marsh migration modeling is also being done to see if the marshes are gaining elevation at a rate that can sustain sea level rise.

“Marsh can move up or out,” explained Alice, depending on the space available. “We have really steep banks so there isn’t a lot of space for the marsh to move.”

In some areas on the reserve, marsh sediment accretion is occurring faster than sea-level rise. In other areas, the rate is lower. Currently, South Slough is part of a nationwide study to see just how much communities have shifted in response to changes in sea level.

“We are getting increased tidal amplitude activity further up the estuary,” Alice said. “Part of restoration is accounting for changing conditions.”

Tunnel Forest

Returning to the forest, we headed south on Tunnel Trail, passing by a massive Sitka spruce and Port-Orford-cedar, before diving into a forest of feathery-leaved western hemlock.

Alice, Jeannie, and I talked mushrooms as we walked beneath the shaded canopy.

Alice also told me of the little blue polypore (Neoalbatrellus) uncommon to the area that can be found only in this section of the forest. “It is one of the largest patched found in the distribution of the species,” Alice remarked, “probably associate with the hemlock.”

Jeannie listed off some of the other mushrooms common to South Slough: coral mushroom, oysters, hedgehogs, king boletes, and golden chanterelles.

Visitors can harvest mushrooms in the reserve for personal use, confirmed Alice.

Soon the trail narrowed and took on the formation of its namesake—a tunnel of vegetation formed by green shrubs rounding above our heads. We walked through the tunnel until we once again reached a more open canopy.

Viewing an Estuary

After about a half a mile, we reached a viewpoint that looked out on the estuary from its forested margin. Marsh grasses covered much of the land in front of us with open water in the distance.

As we were soon to turn away back into the forest, I asked Alice to tell me more about the research that is done at South Slough.

“There is a lot of different research that goes on out there,” Alice replied. “We collaborate a lot!”

In addition to sentinel site data, research projects include: the study of blue carbon sequestration in salt marshes and freshwater wetlands, increasing populations of invasive European green crabs, and decreasing eelgrass populations.

Often the research is coupled with restoration projects, like in the case of eelgrass, a replanting program is underway.

According to Alice, the loss of eelgrass is complicated but seems to be correlated with warm water and air conditions, along with lower amounts of precipitation, with turbidity as a possible secondary driver.

“Standing here it is hard to image we in the middle of a drought, and have been for several years,” Jeannie remarked.

Water quality, temperature, salinity, and turbidity are also all measured at various spots in the reserve through South Sough’s System Wide Monitoring Program (SWAMP). Weather station data is also collected. SWMP is another way South Slough provides data on estuaries.

“We have a lot of research to draw from,” said Alice. “And we use it in a lot of different ways.”  From assessing restoration potential inside the reserve to informing change outside the reserve, South Slough is a data hub for all things estuaries.

Volunteers

At this point, Alice took us on a cut-off trail to one of the parking lots to look for a tagged tree she needed to locate.

One our way, I remarked how few invasive species I had seen at the reserve. Invasive species can be a huge problem in many natural areas. Invasive species are non-native species that outcompete native species for resources, taking over areas and harming the ecosystem. They can also be costly to manage.

“We have a lot of volunteers that help,” responded Alice. “We set up a program for stewards to get together once a month to remove invasive species.”

These volunteers were doing a great job from what I could tell.

Having hiked with Alice and Jeanne for a while now, I was beginning to understand one thing—South Slough values volunteers. In fact, Jeannie is now retired and volunteers her time with Friends of South Slough—a non-profit that facilitates many different projects in the estuary and helps others get involved.

Not too Tough

After the short parking lot diversion, we headed down onto the Hidden Creek Trail and onto a long winding boardwalk. As we walked across the expansive marsh with its dry brown grass, patches of bright yellow and green stood out on the landscape—skunk cabbage!

“I can’t think of skunk cabbage without thinking of my nephew,” Jeannie related. “Show me that frog spinach again, Aunt Jeannie,” had been his child like remembrance of a very memorable plant.

“He knew it was a vegetable and an animal,” she laughed.

Western skunk cabbage (Lysichiton americanus) with its almost prehistoric looking leaves and flowers, is a personal favorite of many. Its foul odor gives it its name, as well as acts like an attractant to scavenger beetles and flies.

“It is also good browse for elk in the winter,” Alice shared. “And you can eat the tuber.”

Many Northwest indigenous tribes considered skunk cabbage a starvation food—eaten primarily when other food sources are scarce. Traditionally, the roots were cooked underground to break down calcium oxalate compounds found in the plant that would otherwise damage or irritate the alimentary canal.

According to Alice and Jeannie skunk cabbage is also high in silica which is abrasive and wears down teeth quickly.

In a “science is really cool moment,” Alice told me about some studies that are being done using teeth to track plant community changes based on the age and micro-abrasions of animal teeth. I wonder what mark a skunk cabbage would leave on my teeth. Does anyone have an underground oven?

Riparian Way

Winding our way along the boardwalk and across another bridge, we found ourselves leaving the marsh and entering a forested riparian area. The trail followed a sandy-bottomed creek that spilled along through a narrow alleyway of grey barked alder—yellow catkins dangling from its limbs.

“I love these little springs,” remarked Alice. “Ripple, pool, ripple, pool,” her words flowed, like the tumbling water.

Looking out on the water, Alice told me about another research project happening in the reserve’s waterways—a lamprey study.

“Lamprey have a very old lineage,” said Alice, having been around 100s of million years—before the dinosaurs. Yet, there is a lot still unknown about the lamprey family, including basic information, like where they can be found.

This is where the lamprey research project comes in.  Essentially, Alice explained, the project involves collecting environmental DNA samples in the water at various sites in Oregon, like South Slough, to look for lamprey. Citizen scientists collect the water samples, and researchers complete the DNA analysis for two of Oregon’s lamprey species—Pacific book lamprey and western brook lamprey.

Both Pacific brook lamprey and western brook Lamprey are present in South Slough. In fact, they have been monitored by ODFW for years. However, in the last 20 years, their populations have declined. They are now listed as Oregon Conservation Strategy Species of greatest concern and need.

Understanding more about where we find lamprey will hopefully help scientists figure out how best to conserve this group of mysterious species.

Sensitive in South Slough

After following the creek for a bit, we reached a junction with Middle Creek Trail. Taking a right onto Middle Creek, we headed uphill back into the mixed-conifer forest and away from the estuary.

As we walked, I asked Alice and Jeanne about other species of concern that might be found in the park.

Alice told me about the endangered western lily—a crimson-colored flower with downward-pointing stamen, and petals that swoop upward.

“It only exists in a certain soil type,” said Alice, making the flower uncommon in the reserve and only viewable in a few undisclosed locations.

Like the western lily, many species face limitations and habitat requirements that restrict their growth. Ensuring the success of these populations takes careful planning.

“It is part of our restoration project to look at the soils, aspect, and slope to think about where we want to plant different species, where they would be most successful,” Alice explained.

Other sensitive species include the less-conspicuous, red or purple-tinged, cream-colored Point Reyes bird’s-beak—a coastal marsh plant threatened by habitat loss, as well as the carnivorous Cobra lily (Darlingtonia californica)—with a naturally limited range.

The Signal

We continued our climb upwards until we reconnected with the Ten-minute Loop Trail that would take us back to the visitor center and our vehicles.

Along the trail, a gap was cut into the forest. Alice explained that there was a lot of dying Port-Orford-cedar and other species that they removed to create the gap. Flowering shrubs, like Oregon grape, were planted in the open space. Bird boxes were put in place on a few tall snags to attract wildlife.  Benches built from the felled trees were placed along the edges of the opening.

Of course, my favorite feature was a massive bat box with the outline of a bat painted in white across the dark surface—a literal bat signal. Though no bats occupied their new home yet—“give it a couple of years,” Jeanne suggested—eventually they will find their way home.

“Appropriate,” I thought to myself—South Slough National Estuarine Research Reserve is a signal to the world regarding the state of our planet. As the Earth faces many challenges, like climate change, biodiversity loss, and invasive species, studying the impacts and efforts to mitigate and adapt to these changes is of paramount importance.  South Slough is doing that good work—helping us understand and protect the planet—the place we call home.

Alice Yeates is the stewardship coordinator at South Slough National Estuarine Research Reserve. She studied ecology and conservation at Griffith University for her undergraduate work before earning a Ph.D. in Ecology at the University of Queensland. She has been at South Slough Reserve for the past 3 years and before that was a lecturer at the University of Wisconsin-Superior and a researcher at the University of Minnesota’s Natural Resources Research Institute. Alice has a passion for plants because their function and importance are often overlooked and not always understood.   

Jeanne Standley worked as a Botanist for the Bureau of Land Management in Oregon and Alaska for 28 years before retiring as the Coos Bay District Noxious Weed Coordinator. Before that, she graduated from Oregon State University with a Bachelor of Science in Rangeland Resources. She is now on the board of the Friends of South Slough