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17th March 2022
...continued from Part 1

Fellow scientists at the meeting were enthusiastic about Lynch’s radical proposal. But at subsequent meetings she quickly encountered a basic hurdle among the other decision-makers. “People,” she says, “had no idea what I was talking about.”


The hyporheic zone is a vibrant place. Its water chemistry, temperature and life-forms differ from those in the stream above and the groundwater below. These kinds of in-between ecosystems are called ecotones—liminal spaces that can harbor great biodiversity because species from neighboring environments mingle there, along with microbes and other critters that reside only in that space.

The tiny beings in the hyporheic zone function as ecosystem engineers, metabolizing inorganic compounds into food for plants and bugs. They move organic matter and nutrients between the zone and riverbed sediments and play a pivotal role in nitrogen, phosphorus and carbon cycles. The hyporheic also helps to regulate a stream’s temperature, bringing in comparatively cooler underground water in the hot summer and warmer underground water in the cold winter.

Scientists have shown how wide and deep a hyporheic zone can reach by mapping aquatic insects and fish embryos found in soil beyond a waterway’s banks. For an urban creek such as Thornton, that lateral reach might extend 30 feet from the stream channel. The depth might be three feet below the streambed.

Straightening a stream and building over its floodplain can destroy the hyporheic zone. It also compounds problems: Rain that falls on pavement and rooftops cannot soak into soil and instead races off these hard surfaces, picking up fine dirt and pollutants as it rushes into the stream. These flows, which ecologists call “flashy,” create a firehose effect that scours the riverbed and the hyporheic material underneath it, laid down over centuries. Eventually what remains is the impermeable underbelly, such as shale or granite. And a straight, armored river channel often cannot contain the flashy runoff; water overflows the banks, flooding the area.

Thriving floodplains absorb potential floodwater. They also slow water, dissipating its energy and reducing erosion. Slow water more readily sinks underground, where some of it will return to the stream over time via the hyporheic, supplying water in dry times. Natural streams with a stable hyporheic have a more balanced flow between winter and summer, helping to maintain water in streams year-round, even in drought-prone areas.

All these processes enable a stream to maintain itself. If the hyporheic zone is stripped away, a stream’s biological gut disappears, and the waterway has little hope of staying healthy—akin to when humans develop serious digestive tract issues because their gut microbiome has been distressed.


Lynch first learned about the hyporheic zone in 2000 at the University of Washington, but she did not appreciate how extensive the zone is until a 2004 field trip into a forest with geomorphologist and visiting lecturer Tim Abbe. She was amazed when they stopped walking and he pointed out that the ground they were on overlaid a hyporheic zone for a nearby stream. “I’m looking around at trees and ferns,” she recalls, “thinking, How is that possible?”

Born and raised in Nova Scotia, Lynch had moved to the U.S. Pacific Northwest and ended up working for Seattle Public Utilities, focusing on stream restoration. The two stretches of Thornton Creek slated for revitalization and discussed at the 2004 meeting were called Confluence and Kingfisher. They totaled 1,600 feet in length. The team chose these spans because they were originally floodplains, and allowing overflow there could greatly reduce problematic flooding along the stream’s longer route. The Seattle Parks Department had already been buying out willing homeowners whose houses flooded along those stretches—five at Confluence and six at Kingfisher—so some of the creek’s stolen elbow room could be restored.

Lynch knew that getting decision-makers to try something new would be hard. Urban stream restorations have big price tags and high stakes—namely, ensuring that people’s properties do not flood. By 2007, after much discussion, the design plans included hyporheic restoration—although it was not approved as a formal part of the project for another seven years. That time line is typical of city projects, Lynch says, which require funding; coordination among landowners, community groups and multiple agencies; and assessments of social justice and equality.

Lynch’s supervisor asked that the work include stream monitoring so scientists could provide data to inform subsequent projects. Paul Bakke, then a geomorphologist at the U.S. Fish and Wildlife Service, did baseline measurements, which confirmed that Thornton Creek’s hyporheic zone had been almost completely scraped away. The utility hired Seattle-based Natural Systems Design, a science and engineering firm that restores waterways. Lynch teamed Bakke with the firm’s lead engineer, Mike Hrachovec, to create the innovative design.

The restoration was personal for Bakke, who had grown up in the 1960s and 1970s along Thornton Creek, fishing for cutthroat trout and playing with water skeeters. Just before he entered high school, the city issued permits for condos along the creek’s edge, cutting off his access to the water. “These old haunts that I really loved, that were my sort of wilderness ... were suddenly not just blocked but being paved over,” he says. “It was very upsetting.”

Hrachovec also frequented streams in his youth, in South Dakota’s Black Hills. Nevertheless, when Lynch paired them up to redesign Thornton Creek, the two men found collaboration rough going. In one battle, Bakke wanted to put larger gravel on the streambed so water could move more easily into the hyporheic. Otherwise, he feared, urban dust washing into the creek could plug up the downward flow. Hrachovec worried that large gravel might convey too much water underground, drying out the surface stream in summer and killing fish. This kind of uncertainty is one reason it can be hard to get a city to try something new.

Stream shape, gradient, water speed and debris also influence flow into and out of the hyporheic zone. To sort things out, the team ran tests using computer simulations and in a large sandbox, modeling stream dynamics and trying different rock aggregates, curves and wood placement to drive water underground. Satisfied at last, and with other city requirements in place, Seattle put out a call for bids in early 2014. Then, in May 2014, just before construction was due to begin, the Seattle Public Utilities project manager raised budget concerns because another project was running over. “In front of my eyes,” Lynch recounts with incredulity, “he says, ‘What’s this hyporheic thing?’ And he just cut it.”

Lynch told the manager how crucial the zone was and argued that the hyporheic elements accounted for only $300,000 of the two sites’ combined $10.5-million budget. She told him the investment—for excavation and materials such as boulders, gravel and finer sediment—was likely to pay off quickly. Her team had determined that rebuilding the zone would reduce the need to spend $1 million a year on average dredging sediment from a nearby stormwater pond built to absorb heavy runoff.

She also reminded the manager that the monitoring would provide lessons on how to reconstruct urban streams to something closer to their full complexity, making Seattle a leader in this work worldwide. In the end, they negotiated. Lynch was able to keep the Confluence hyporheic restoration intact; the Kingfisher reach was shortened by 25 percent.

In summer 2014 the bulldozers moved in. Hrachovec and his team scooped out generous curves in the spaces reclaimed from the houses, in spots widening the creek from four or eight feet to 25 or 30 feet. To bring the creek bed to its former elevation and reintroduce material that would hold the hyporheic zone, they layered in sediment and gravel nearly eight feet deep. Hrachovec and Bakke inserted logs of different sizes into the water at precise angles—some partly buried, some crisscrossing the streambed—creating tiny waterfalls, plunge pools and pockets of nearly still water that create hydraulic pressure that can force water down into the zone. These meticulously placed logs and boulders, known as “hyporheic structures,” also create eddies and pockets of slow water that provide safe havens for juvenile fish and bugs—all meant to emulate features of a natural stream.

The Kingfisher reconstruction was finished by that fall and the Confluence by spring 2015. The creek’s flow slowed, so sediment dropped out of the water column and began refining the stream’s shape and bed. That action also reduced what had been rapid downstream sediment accumulation that the city had removed regularly at great expense. Over the next five years gravel and silt gradually built up behind the wood barriers, creating gentler grades.

The monitoring allowed Bakke and Hrachovec to track water flow by sensing temperature and following tracers. They confirmed that water was indeed moving down and through the hyporheic zone. In a 2020 paper, they reported that water was mixing there at 89 times the preconstruction rate. Data analysis proved the stream was working as Bakke and Hrachovec—and nature—intended.

But was that flow also supporting life and reducing pollution?


Restoring a stream’s natural shape can encourage displaced plants and animals to move back in. In many cases, however, only some species return. And because the gravel and sand the team installed were sterile territory, Bakke thought they might need a biological jumpstart.

If a species is missing from an ecosystem, our instinct is simply to reintroduce it. But ecologists are painfully aware of cautionary tales such as stocking a desirable trout that inadvertently brings pathogens along with it. Even bringing back a native plant can shake up a system that has adjusted to its absence.

Kate Macneale, an environmental scientist for King County, where Seattle is located, understands this lesson. She monitors insects as a measure of stream health, rating them on what she calls the “bug score.” Macneale had found a clear correlation between urbanization and lower bug scores; some species, she figured, were too sensitive to survive.

A few years ago an experience made her rethink that conclusion. Vandals had destroyed an experiment she had set up in Seattle’s Longfellow Creek, which released what had been captive bugs into the “wild” of the urban stream. Two years later she was sampling fish there and found one of the bugs, a caddisfly, in a fish’s gut. Caddisflies live only for a matter of weeks, so it could not have been an individual from the unintended release: it must have been a “grandkid of that individual,” she says. “I couldn’t believe it.”

Macneale realized that some insects in reconstructed streams might be missing not because they cannot hack the conditions but because there were no nearby insects around to recolonize the water. The idea that life will return to restored creeks relies on critters migrating from healthy upstream habitats. But with Longfellow Creek, Macneale says, the headwater “is literally a Home Depot parking lot.” If organisms are to recolonize restored streams, she says, “we may need to help them out.”
...continued in Part 3