OSO — Jason Griffith and Robert Lamb pulled on their wetsuits and waded into the river.

Griffith and Lamb both work for the Stillaguamish Tribe of Indians’ Natural Resources Department. They were setting out on a four-mile snorkeling trip the morning of July 16 on the North Fork Stillaguamish River to count fish, especially Chinook salmon and other threatened species that were thought to be lurking in some of the river’s deeper pools prior to spawning season.

Griffith, a biologist, and Lamb, a fisheries technician, strapped pieces of white vinyl to their wrists to take notes on and stuck golf pencils up their sleeves. Then they waded out to the center of the channel — where it was about three feet deep — dropped face-down into the water and floated downstream.

The Stillaguamish is home to three species listed as threatened under the Endangered Species Act: Chinook salmon, steelhead trout and bull trout. In recent years, however, the river suffered two blows that have threatened the survival of those species.

First came the Oso mudslide on March 22, 2014. In addition to killing 43 people and cutting off Darrington from the rest of the county, the slide dumped tons of sediment into the river, turning the north fork opaque gray.

After the bodies of all the victims had been recovered and Highway 530 reopened, one of the concerns of biologists was what the silt was going to do for fish habitat.

There were signs the river was rebounding from the slide.

Then came the second blow: record low winter snowpack combined with high temperatures and drought caused record low water levels this summer just as the salmon started to return.

Legendary river

The Stillaguamish has a storied past, home to what at one time was one of the best wild steelhead runs in the U.S.

Western writer Zane Grey hooked one of his first steelhead in Deer Creek near Oso, and the river winds through bucolic rural valleys between Darrington and Puget Sound.

But the Stilly also is perennially challenged, starting with the retreating glaciers that carved its valley and deposited loose sandy soil prone to erosion and landslides. Then an eruption of Glacier Peak about 13,000 years ago cut the north fork off from its original source in the Sauk River, which now drains the central Cascades into the Skagit River.

Human development in the form of logging on the riverbanks, dikes built to protect farmland and an influx of people into towns on the lower reaches have all had contributed to less-than-ideal fish habitat: the river is shallower and warmer than many others in the region, and prone to flooding.

“The Stillaguamish is, unfortunately, cursed with a lot of sediment and a system that gets lots of floods compared with the Skagit right next door,” Griffith said.

Chinook populations also have lower survival rates in the Stillaguamish, he added.

The state Department of Fish and Wildlife provides forecasts for each year’s run of different salmon species, and the numbers tell a tale of a river faced with challenges.

For example, the department has estimated that 525 Chinook salmon will return to the Stillaguamish River this year, compared with 4,159 on the Snohomish and 11,796 on the Skagit.

The estimates for Coho are also lopsided, with 31,263 expected in the Stillaguamish, compared with 151,549 in the Snohomish and 121,426 in the Skagit.

Even the plentiful pink salmon run this year, estimated at 210,000 for the Stillaguamish, pales in comparison to more than 603,000 expected in the Skagit and 1.6 million in the Snohomish. In past years, however, there have been runs of up to 1 million pink salmon in the Stilly, Griffith said.

The Stillaguamish Tribe has not fished for Chinook commercially since 1990, and its hatchery operations are focused on restoring wild runs of Chinook and Coho, Griffith said.

It’s part of the tribe’s recovery program for those species, as well as for chum, which return in November.

The tribe will attempt to net 120 returning Chinook in August and 100 Coho in November and December, Griffith said, with the intent of releasing up to 200,000 juvenile Chinook back into the river next spring and about 30,000 Coho the following year.

Trying to rebuild wild runs of fish was challenging enough without having to counteract the effects of the one-two punch of a major mudslide and record drought.

A silted stream

The Stillaguamish had always been silty. The South Fork gets a lot of sediment from the Gold Basin and Trangen Meander landslides. On the North Fork, the Oso slide area has been a source of silt in the river going back decades, and another landslide above Deer Creek was active in the 1980s and early 1990s, said Fish and Wildlife biologist Pete Verhey.

“It sent a lot of material into the creek and river with long-lasting effects on habitat,” Verhey said.

“It had just started to clear up and then this slide hit,” he said, referring to Oso. “It will take years to recover again.”

Since March 22, 2014, the U.S. Geological Survey’s stream gauges have measured a cumulative total of 800,000 tons of sediment that has eroded from the Oso slide zone, said Scott Anderson, a hydrologist with the agency’s Washington Water Science Center in Tacoma.

Most of that sediment has been composed of fine silt and clay that formed the bottoms of glacial lakes, Anderson said.

“Because it has been so fine, a lot of the material looks to have transited through the system fairly quickly,” Anderson said.

Data from the USGS show an initial spike of turbidity occurring shortly after the slide, which then tapered off after a couple of months. A second spike occurred in the fall of 2014, when the rain eroded more silt from the slide zone.

“The first two months, that process of overtopping that deposit and chewing out that channel did a lot of work,” Anderson said.

While the fear was the fine silt would coat the river bottom and smother any spawning grounds downstream from the slide, it’s possible that worst-case scenario was avoided.

Part of Verhey’s job is to survey steelhead redds in March and Chinook redds in the fall. In 2014, he spotted some evidence that the fish were swimming through the opaque current to the upper reaches of the river, and also that they were nesting in tributaries they normally would have avoided because the quality of the habitat isn’t as good.

In 2015, however, the water is much lower and clearer, and Verhey spotted more than 520 steelhead redds below the slide area. That wasn’t even possible in the main stem of the river in spring of 2014, when the water was the color of concrete from all of the slide runoff. Verhey counted 362 redds in the North Fork and its various tributaries last spring.

“It would seem the impact of the slide on spawning was sort of short-term,” Verhey said.

There is still a significant amount of sediment in the water from Oso, most of it washing out during the rainy winter months. Anderson estimated that up to 60 percent of all the sediment detected at the USGS gauge near Whitman Road originates in the mudslide.

“It’s still a very significant sediment source and will be for some years to come,” he said.

Dry and hot

The bigger challenge for 2015 has been the drought. With 99 percent of Washington state in severe drought conditions, rivers have had record low flows and high water temperatures.

This month the state restricted fishing on more than 30 rivers due to the drought, including a ban on fishing the entire length of the Stilly from Marine Drive near Stanwood all the way to its upstream sources.

The USGS’s gauge in the North Fork Stillaguamish near Arlington recorded average flow of 188 cubic feet per second on July 22, well below the average of 680 cubic feet per second for that date over the past 86 years of record-keeping.

Low water also means a less healthy stream for fish, with shady banks that normally provide cover left high and dry above the water line. Some tributaries have been cut off from the main channel, creating small oxbows.

The water in some places is only ankle-deep, and fish expend a lot of energy crossing those places, said Jennifer Whitney, a biologist with Fish and Wildlife.

Historically, there was a lot of wood in the Stilly, Griffith said, and since 1999 the Stillaguamish Tribe has built logjams in the river to create more pools for fish.

There are tree-planting and other habitat restoration efforts under way, but those are slow undertakings.

“Habitat restoration is a fairly involved and expensive process,” Whitney said.

Adult fish returning to the Stillaguamish will compete for that limited habitat with each other and juveniles from previous years’ hatches that haven’t yet migrated to the sea.

“We don’t know what the effects will be, but it’s tougher than usual conditions on them,” Whitney said.

The Stilly has always had challenges with increased water temperature because it is so shallow, said Ralph Svrjcek, State Department of Ecology water quality planner.

“Right now, when we’ve got less water than normal, we need now more than ever to keep that water cool,” Svrjcek said.

Water temperatures above 70 degrees can be hazardous for salmon, and spikes of up to 79 degrees have been recorded for short periods during the day in the lower river where there is less shade. The North Fork, fed by more groundwater streams, is generally cooler, with spikes as high as 75 degrees during the most recent heat wave, but temperatures as high as 80 and 81 degrees have been recorded in the South Fork, the Stillaguamish Tribe’s Jason Griffith said.

The high temperature makes fish tire out more quickly, suppresses their immune systems and can make them more vulnerable to predators or poaching.

Even an angler who accidentally hooks a Chinook and tosses it back might exhaust the fish while landing it, increasing the chances it won’t survive until it can spawn, Griffith said.

“We’ve seen temperatures that could be lethal if they were sustained,” he said.

“If fish can get up into the North Fork, the temperatures aren’t lethal, but they’re stressful during the day,” he said.

The suspicion is that the lower river has become a thermal barrier to fish and the salmon are waiting out in Port Susan for the water to cool off before attempting to migrate upriver. That leaves them susceptible to hungry seals and sea lions.

When Griffith and Lamb did their snorkel count on July 16, their observations supported that theory that the fish just weren’t coming up river yet.

They counted a total of 75 Chinook, 77 bull trout and 15 steelhead in one four-mile stretch of the upper river. Most of those Chinook were concentrated in a single deep pool, and several other pools and holes were nearly empty of fish.

While the bull trout and steelhead numbers were more in line with expectations, there normally would be about 150-200 Chinook in the North Fork, Griffith said.

“In general, it’s fewer Chinook than we’re used to seeing this time of year,” he said.

There haven’t been any confirmed reports of fish kills yet — and Fish and Wildlife has put out the word to the public to report any die-offs — but in this year’s stressful conditions, they’re trying to be careful.

“We’re kind of concerned, but don’t have enough data to say whether it’s bad or not,” Griffith said.

The real proof will come in the spring, he said, when the Chinook hatch, and over the next two to five years when fish that hatch this year are expected to return to the river.

Chris Winters: 425-374-4165; cwinters@heraldnet.com. Twitter: @Chris_At_Herald.