When the tide is out, Skagit Bay looks like you could walk across the mud almost all the way to Whidbey Island, said Mike Hayes, U.S. Geological Survey fisheries biologist.

The Skagit River’s North and South forks, as well as other streams and drainage ditches, carve channels of water in the mud flats.

The sight of the bay at low tide made Hayes wonder: What do juvenile salmon and other fish do at extremely low tide? Where do they go as the tide changes? Are they constantly using bay’s eelgrass?

Those among of the many questions about the Skagit Bay and salmon that scientists can’t answer yet.

Hayes and Steve Rubin, another USGS fisheries biologist, are trying to answer some of those questions about fish, including chinook salmon and forage fish, such as herring, sand lance and surf smelt, which salmon prey on.

Hayes, Rubin and two other USGS fisheries biologists spent this past Monday and Tuesday, April 20 and 21 in the bay netting salmon and their prey fish, as well as other species.

They’ll return monthly to sample 40 spots with the same four eelgrass beds until September. It’s the second year they have sampled fish from April to September. 

“We’ve been out there in hail storms,” Hayes said.

They call it quits when the bay is too rough for their 16- to 18-foot boats.

Hayes said he hopes their work will help determine how juvenile chinook salmon and other fish use the eelgrass beds in the bay. The wild chinook salmon are listed as threatened on the Endangered Species List.

“The big goal is to see how land and river management decisions will affect the nearshore (habitat),” Rubin said.

Scientists consider eelgrass beds an important part of the marine ecosystem. The sea grasses provide food and shelter for a variety of species including forage fish.

Many scientists focus their research on the Skagit River Delta because it’s the southern-most river where all five species of Pacific salmon spawn. Although the Skagit has water quality issues, the contamination is not to the degree seen in other rivers in the Sound, especially in the South Sound.

“It’s a unique river, for one,” Hayes said. “It’s in relatively good shape.”

Rubin said that his and Hayes’ work may give resources managers a baseline that will allow them to make comparisons after they make decisions that may affect the river.

Hayes said that the data will help decision makers assess whether their land use will affect those nearshore ecosystems. If something were changed in the river upstream from the bay, then that might affect the flow of fresh water, which could affect the bay’s sediments and its eelgrass. That in turn could have a positive or negative impact on the fish in the bay, Hayes said.

“It’s all linked, of course,” Hayes said. “If those actions create reactions they may or may not affect salmon or smelt.”

The four distinct areas where Hayes and Rubin catch fish were selected because of the difference in the composition of the eelgrass beds and influence of the river’s forks on the sea grasses. In some cases the vegetation is fragmented and in one it is continuous.

The differences between the areas will help scientists determine which types of eelgrass beds are more important for the various fish species, Hayes said.

Their work is part of a number of studies being conducted by USGS in the Skagit delta and bay as part of the agency’s Coastal Habitats in Puget Sound program. The program studies the effects of urbanization on nearshore ecosystems and looks at recovery on Elwha River and restoration in the Skagit delta and the Whidbey Basin.

In the Skagit delta, USGS scientists also are studying river flow and silt deposits, the mix of freshwater with saltwater and how migrating juvenile salmon use the delta and bay, as well as mapping the layers of sediments in the delta and bay.

All these studies are being conducted to improve scientists’ understanding and ability to predict how land use and climate change will affect the river and the near-shore habitats, said Eric Grossman, the USGS research geologist who is overseeing the work in the Skagit delta, in an e-mail.

Hayes, Rubin and their crew take two boats into the bay and use portable global positioning system units to located their sampling sites. They then deploy a 150-foot-long lampara net that is roughly 20 feet deep.

With the ends of the net attached to each boat, the scientists create a circle with the net and then haul in their catch. After they measure and record each of the fish they catch, they release them back into the water.

Last year, Hayes and Rubin used the same techniques to conduct a pilot study in the bay and recorded a total of 24 species, including four of the five Pacific salmon species. They didn’t net any sockeye. They caught the most chinook in July and August. (I don’t have breakdown on hatchery v. wild. They did run the scanner to track the hatchery fish.)

This year, they will return to the same four areas, and they also plan to sample locations where there isn’t eelgrass, which can be used for comparison, Hayes said. They also are photographing the sample spots with an underwater camera to compare the density of the eelgrass with the aerial photos that helped them select their four locations.

Other groups and agencies are also conducting salmon research in the area, including the Skagit River System Cooperative and National Marine Fisheries Service.

Hayes said that he hopes all the studies will provide a complete picture of how salmon and other fish use the delta and bay.

Hayes and Rubin’s study is funded through the end of this year. Although the scientists say it’s important to continue the work, agency officials haven’t found the money to pay for the study next year, Grossman said.

Besides answering some of those questions about fish, Hayes and Rubin’s work has other rewards.

“One day we were trying to get out of the wind and hugging the Whidbey shore, and we saw more than 70 bald eagles,” Hayes said.

n Marta Murvosh can be reached at 360-416-2149 or . 

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