A recent report from the Puget Sound Partnership helps us understand the difficulty of restoring the Puget Sound ecosystem. What caught my attention in the State of the Sound report was that after 20 years of protecting and restoring streams, wetlands, shorelines and estuaries, we have not increased overall fish and wildlife populations, and some remain in a downward spiral. (Our Water Ways, Nov. 3).

Several reasons have been given for the disappointing findings, including ongoing habitat losses from an increasing human population in the Puget Sound region. Clearly, there is a need to find ways to accommodate growth while protecting the remaining functional habitats.

At the same time, I would like to focus some attention on the restoration side of the equation. It seems we may not yet understand what it takes to restore habitats in ways that allow the food web to thrive, thus allowing increasing numbers of higher predators, such as birds, salmon and killer whales.

I recently wrote about some bug-seeding experiments underway in several streams that flow through urban areas in Seattle (Encyclopedia of Puget Sound, Oct. 21). For some reason, populations of aquatic insects known to provide food for salmon were not recovered to the degree expected, given efforts to restore the stream channel, remove invasive weeds, plant native vegetation and reduce pollution to improve water quality. As a result, researchers launched a project of transplanting important insects from a healthy stream. So far, results are mixed.

Katherine Lynch, urban creeks biologist for Seattle Public Utilities, points out that restoration projects are often limited in scope and extent.

“The reality,” she told me, “is that when you go in and do restoration work, you are only doing a short reach. These projects (in Seattle) are a way of exploring what works and what doesn’t.”

To restore or improve salmon habitat in a stream, the challenge is to understand what has been broken in a complex interactive system. Factors include water quality, water flow, clean gravel, and the intricate interactions of the food web — from microscopic organisms to large fish, including predators that eat young salmon.

Take water quality, for example. Until recently, nobody knew what was killing adult coho salmon that found their way into urban streams. Scientists tracked the problem to stormwater entering the waterways from roads and highways. Then last year, thanks to advanced analytical tools, researchers were able to identify the killer compound, which comes from a chemical found in tires. Until then, nobody seemed to know anything about this chemical, let alone thinking that tires might have lethal properties. (EoPS, Dec. 3, 2020).

The discovery opened a lot of eyes to questions about how to identify “clean” water and the prospect that unknown chemicals may be causing unidentified problems in waterways throughout Puget Sound and across the country. The tire-related compound has been found to have lesser effects on steelhead and Chinook but no apparent effects on chum or sockeye. Work continues on varieties of species that might be exposed to road runoff, not just in urban areas but practically everywhere.

The discovery that dying coho could be linked to a tire chemical, known as 6PPD, and its deadly oxidation product, 6PPD-quinone, raises even more questions about the sublethal effects of other chemicals not yet identified. Standard water-quality tests cannot capture the toxicity of unknown chemicals in a stream. Even biological tests, such as using aquatic invertebrates (EoPS), may not reveal the toxic effects on vertebrates — such as fish, birds and humans.

Besides water quality, water flow may be a critical ingredient in stream restoration. I’ve been hearing a lot lately about hyporheic flow — the flow through gravel beneath a stream bed — and its effects on temperature (EoPS, Aug. 19) and oxygen supply, even its ability to filter contaminants.

In Seattle’s Thornton Creek, an understanding of hyporheic flow led to an engineered design in which the stream channel was dug out — up to 8 feet in some places — and replaced with gravel, according to Paul Bakke, owner of a firm called The Science of Rivers who monitored the physical functioning of the project. Rocks and logs were lodged in the streambed along with an impermeable barrier that forced the flowing water deep into the underlying gravel. The water plunges down into deep gravel, coming back up and diving down again several times in each of two reconstructed portions of the stream. The gravel helps filter fine sediments from the stream, but the configuration of the channel allows these fines to be washed on downstream during high flows, Paul explained. Organic chemicals in the water adhere to deeper gravel, where large fractions of chemicals are broken down by microbes.

A team of researchers affiliated with the Center for Urban Waters in Tacoma evaluated the fate of 83 chemicals moving downstream in Thornton Creek. Included were the toxic tire chemicals. The hyporheic flow path substantially improved water quality, according to the findings published in 2019 in the journal Water Research.

After construction of the hyporheic zone, Paul found that the vertical flow rate in the new gravel was 89 times higher than in the previous streambed, which had been impounded by a heavy sediment load. In fact, the fresh gravel produced a flow rate 17 times higher than in a forested stream in the mountains of Idaho.

The newly engineered stream also included a floodplain, created by removing flood-prone houses from the area. During high flows, sediment-containing water moves from the stream channel into the floodplain, where lower water velocities allow the sediment to settle out. That helps to protect the stream channel from excess sediment.

According to Paul, the key to success was rebuilding the stream by carefully choosing the width and depth of the channel and floodplain. The new configuration balances the forces of erosion and deposition, thus maintaining the channel in a more natural condition. In addition to Paul, the lead channel designer was Mike “Rocky” Hrachovec, owner of Natural Systems Design. For details of the design, check out the article in Research Outreach or the more technical article in the journal Water.

The ability of the restored sections of Thornton Creek to clean themselves, increase oxygen levels and mediate temperatures has led to a healthier condition, despite the urban setting in North Seattle.

In 2018, four years after construction, a female Chinook salmon swam warily upstream. With a male Chinook standing by, she deposited her eggs, which were quickly fertilized by the male.

“They spawned,” Katherine said. “We had never seen salmon spawn in the project region.”

A lack of funding and the COVID-19 pandemic have prevented further in-person monitoring of salmon movements, but new methods of testing for the presence of salmon are being developed. Seattle officials hope that salmon populations will increase in Thornton Creek, where beavers have established a new dam on the project site.

Along with new research into stream ecology come better methods of stream restoration and the chance that salmon and other species will find a suitable home. The same can be said for such “adaptive management” in relation to shoreline, wetland and estuary projects that bring us closer to a true recovery of our native species.