Category Archives: fish

Juvenile Salmon Use of Nearshore Habitats in San Juan County

Tina Wyllie-Echeverria

Collaboration with Eric Beamer and Kurt Fresh (tows), and many students/volunteers

1950-2006, about 50 sites around the San Juans have been sampled and have found juvenile salmon.  Of 656km of SJI shoreline, 430km is rocky beach.  Tow nets (164 tows at 37 sites, monthly from Apr-Sep) caught juveniles of 5 species and 785k fish overall; 657 beach seins at 27 sites caught juveniles of 5 species and~100k fish overall.

% of catch (seine, tow): sculpins (29%,0%); smelt, sand lance, herring (17%, 98%); salmon (16%, 0%?); surf perch (16%, 0%); gadids (7%, <1%); hexagrammids (lingcod, kelp greenling 2%, <1%).

Chinook mostly present apr-sept (mostly august), about 2 months later than in Skagit estuary.  Juvenile salmon  are common Mar-Sept and were present year-round in all environments at all sites.

Along west side, catch was ~10x higher near Eagle Point than near Henry Island, but Rosario side was generally dominant (especially herring).

Nearshore Chinook use in Strait of Juan de Fuca

Anne Shaffer

Focus on central and western strait, trying to identify restoration actions associated with dam removal on the Elwha.   The area is also an important migratory corridor, ultimately seeing about 85% of the outflow from the Salish Sea.  430 seines in many habitat types over last 18 months, 16 snorkel surveys, 2 yrs surf smelt spawn surveys.

Embayed shorelines, spits, and bluffs have higher diversity than lower rivers, but only at drift-cell scale.  Took genetic samples to see if PS chinook use the area.  63 juvenile chinook, 46% came from Elwha/Dungeness, 44% from Columbia, and 10% from inland WA.  Smelt densities change dramatically between years, usually peaking between April and September.   Kelp beds have higher densities of fish.

Fish Response to Shoreline Habitats

Jason Toft

Comparing along-shore snorkel surveys between cobble beach, sand beach, rip rap, deep rip rap, and overwater structure.

We see biggest difference when you have sub-tidal modifications.

Gastric lavage of juvenile Chinook: insects dominate in shallow habitats, plankton/benthic dominate when shoreline is steep.

At Olympic sculpture park, we looked at pocket beach and subtidal bench before and after construction.

Pocket beach example:

  • 94% juvenile salmon and few predators
  • lots of post-larval fish ~3cm

Duwamish turning basin example:

  • Chinook only use deeper portions; chum use both shallow and deep

Seahurst park (invertebrate example) where they took away a sea wall:

  • higher diversity in first year, though abundance is still lower than reference site

Nearshore distribution and size-structure of juvenile salmon and forage fishfrom the observations and modeling on watersheds, marine waters, and marine biota. These talks will focus

Elisabeth Duffy*, David Beauchamp

Juvenile salmon are moving through Puget Sound (PS) from April-July.  By end of July most have made it to the deep ocean.  Percent of fish from hatcheries is about 50% in N PS and 90% in S PS.

Nearshore fish comunity: herring and perch up north, hatchery salmon dominate in the south; salmon are 30-130mm, herring 130-160cm, sand lance 100-130cm; north diets dominated by insects, south diet by crab larvae, euphausids; predators drive early mortality and salmonids dominate (cutthroat target smallest juveniles)

Overall, marine survival has been really low, and lowest during pink years.  The bigger the fish are in July, the better their marine survival.

Where do we go from here?

  • synthesize data across Salish Sea
  • Prey supply (zooplankton) is a big data gap

Forage fish spawning habitat selection

Theresa Liedtke et al focuesd on 2 forage fish species: Pacific sand lance and Pacific herring

Initially focused on Liberty Bay (Poulsbo, WA; today’s data) with non/urban coastline; now working at Possession Point (s Whidbey Island) to get higher wave action and feeder bluffs.  12 sand/sediment samples, 500ml samples preserved eggs.

Findings: 40k eggs in Liberty Bay, 83 per sample; predominantly surf smelt (94%), sandlance and rock sole remaining; >60 eggs/sample called “high egg count” sample and included in a regression.

High egg counts associated with: shell fragments, high position on beach, and proximity to sediment source (eggs moved by wave action?).  If you had all 3, you had 82x chance of finding eggs on that beach.  Not associated: armoring, shade, freshwater input, upslope development.

Thus far, no eggs at Possession Point.

K. Dodd: dynamics of Port Madison fish

Data from N end of Bainbridge and repeat trawl survey from Tom Quinn’s UW class (~20 trawls/year from 1991-2008, over 2nd weeend in May, 4 depths (10-70m)).  Time series started just after 1989 fish closure, so expected increase in catch rate over time, but that wasn’t the case.

Catch anomaly shows an actual catch that is higher than expected (based on number of trawls completed compared with historical average for that depth and location).  Catch anomaly decreases for rockfish and slendersole, but increased for english sole.  Some species show up episodially: 1990 pulses of shiner perch, mid90s pulse for Pacific hake, big tomcod pulse in 2000, and 2003-4 for walleye pollock.  No trend in ratfish.  English sole was most abundant overall.

It’s unclear why these declines have occurred.  WDFW has sometimes seen increases for the same species and years in other parts of Puget Sound.

Alejandro Frid: rockfish & predation risk theory

Vancouver Aquarium Marine Science Center

Focusing on quillback rockfish and interactions with one of their prey, 3 genera of demersal shrimp which show strong spatial association.  An example from 8 reefs in Howe Sound and adjacent Georgia Strait, depths 14-25m, daytime, 10 Jul – 18 Nov, 2008

Lingcod are the main predator of quillback rockfish.  Estimated biomass in Strait of Georgia down 90% in last 100 years, majority in Howe Sound are <75cm.  Smallest quillback should have strongest avoidance of encounters with lingcod at the expense of access to the shrimp.  Counts per minute (CPM) of small quillbacks rise with shrimp and fall with lingcod.  Large quillback CPM also rises with shrimp, but doesn’t alter with rising lingcod.

If we control for structural complexity of the habitat, then shrimp CPM decreases with rising activity of rockfish.

Predators should be managed not for demographic persistence alone, but for the maintenance of risk-driven ecological processes.

Anne Beaudreau on lingcod in the San Juan Islands

What are the interacting relationships between rockfish, the lingcod that eat them, and the fishers who take lingcod (and rockfish)?  In reserves we can look at predatory role of lingcod without fishing pressure.  We can also look at differences in lingcod population structure and feeding between non/reserves.

Most samples from central San Juan Channel in rocky habitat.

Body size:

  • non-reserve: 35-80cm, mean ~45cm
  • reserve: quite a few large females, 80-120cm.

Catch rate: in reserves we had many more days when we caught >3 lingcod/hour.

Acoustic telemetry synopsis

  • Limited movement: 8/9 tagged lingcod never left reserve
  • Diet composition: rock fish are 20% of diet in reserves, only 5% in non-reserves (maybe because there are more rockfish in reserves, or maybe larger rockfish in reserves eat more rockfish, or maybe there are habitat differences)
  • Estimated rockfish consumption (modeled): consumption of rockfish in reserves may have been 5x non-reserve, with implications for how to recover rockfish!


  • Pop structure differs between non/reserves
  • diet variations suggest local diffs in fish communities
  • there are unexpected ecological consequences of creating reserves…
  • match scales of research and management (got to get down to pretty small scales!)

Northern resident bounty this year?

This just in from

Forecasts are great for the Queen Charlotte’s and the Nushagak in 2009

Canadian Fisheries claims the water temperature is the coldest in 11 years and the ocean conditions are perfect for setting up huge runs of returning Chinook and Coho for 2009.  In 2005 the Nushagak had over 300k returning Chinook – this year will be the returning fish from that run, coupled with terrific ocean conditions equates to a banner year in 2009

What does this mean for the southern residents?

No mention of orcas in Columbia salmon injunction email

The appended email from the “Columbia and Snake River Campaigns” provides a helpful synopsis (despite the awful typos) of recent legal activity regarding the management of salmon in the river system.  I find it noteworthy that the supporting quotes (and the email overall) make no mention of killer whales and their need for Columbia/Snake salmon.  It’s all about jobs in the fishing industry; there’s no mention of jobs in the whale watching industry.

Does anyone have good stats on the value of each industry?  I have a value in my head for the whale watching industry (from a 1990’s era article that I don’t have handy) of about $90 million per year for the US/Canada whale watching industry.  I’m not sure if this is direct revenue from whale watching, or integrated across all business driven by the whales existence.  A super-cursory search for salmon industry value turned up the newspaper article that suggests $60-300 million per year for West Coast (US) commercial and sport fisheries and associated business.

Salmon advocates work in court to restore salmon and Northwest jobs

Bobby Hayden,

Dear Scott,

Last week, the State of Oregon, along with fishing and
conservation groups within the Save Our Wild Salmon Coalition
asked a federal judge for help to improve river conditions for
endangered Columbia-Snake salmon and to begin rebuilding jobs
supporting West Coast fishing families and the salmon economy.

This past June, these same groups filed a lawsuit against the
Bush administration’s May 2008 Federal Salmon Plan for violating
the Endangered Species and Clean Water Acts. Over the last eight
years, courts have ruled the previous three federal plans
illegal for refusing to follow the science and the law and
failing to save and restore healthy runs of salmon and

Last week’s request to the judge was filed in U.S. District
Court (called an “injunction”) and seeks specific protections
for Columbia-Snake River salmon and steelhead in 2009. If and
how these measures are implemented depends Judge Redden’s ruling
on the Administration’s 2008 Salmon Plan. Many of the requested
measures, such as increased water flow and spill over the dams,
help mimic a real river and have proven to be effective
short-term solutions to aid salmon and support local fishing

On January 16, 2009, Judge Redden will hear oral arguments from
both sides on this important case. This request for the court to
require specific measures to help salmon in 2009 and beyond will
not be answered until after the Judge first rules on the
lawfulness of the 2008 Federal plan. made last week is unlikely
to be addressed until after the court rules on the merits. A
ruling on the injunction would be made sometime after
mid-February 2009. Please read below for more information. Stay
tuned for more updates as this moves forward.

What you can do:
While a favorable decision on the injunction will be a real
boost for salmon and West Coast fishing communities, it is not a
lasting solution. We need leadership from members of Congress,
both in the Northwest and across the country. In 2009 they will
have a great opportunity to move legislation begins to restore
endangered Columbia and Snake River salmon, creates new jobs,
and ensure a truly clean and affordable energy future.

If you haven’t already sent a quick message to your members of
Congress, please do so now:

Recent press on the issue:
Times-News – Twin Falls, ID: Salmon advocates propose dam
spills, higher flows

Associated Press (in the Oregonian): Salmon advocates ask for
more water over dams

Recent quotes from Northwest leaders:

Glen Spain of the Pacific Coast Federation of Fishermen’s
“This is a jobs issue for the fishing industry, pure and simple.
The Snake and Columbia River dams still kill millions of salmon
and devastate salmon-dependent communities all up and down the
coast. Frankly, the Bush administration’s policy has been
nothing but denial and delay. With the new Obama administration
and next year’s Congress, we have a new opportunity to recover
these once-mighty salmon runs before it is too late. Otherwise,
we will see economic devastation in the Northwest like never

Liz Hamilton, executive director of the Northwest Sportfishing
Industry Association:
“We need the court to make sure we keep salmon on life support
until we can get them to the recovery room. We saw improved
salmon returns this year only because in 2006 fishers and
conservationists fought tooth and nail in court to secure
protections for these fish. But the Bush administration has
already stripped away these protections, calling for lower flows
and less spill. We’re fighting to make sure that this year’s
good news will not become just a fleeting memory.”

Harvey Morrison, Spokane contractor and steelhead fisherman:
“It’s important to understand that what is being proposed in
this preliminary injunction is not a long-term solution to the
economic crisis in the Northwest. It’s a stop-gap measure that
we must rely on because the Bush administration has left us no
other choice We need our Northwest lawmakers to show leadership
and bring people together so that we can find lasting solutions
that will secure fishing jobs as well as important
transportation needs for farmers in Inland Northwest.”

Bill Sedivy, executive director of Idaho Rivers United:
“This [request] is designed to buy our salmon and steelhead time
while we get to the business of developing a clean energy
infrastructure that is not dangerous for salmon and steelhead
and set the table for broad regional discussions and
negotiations that are going to lead to a final and successful
salmon solution someday.”


The recent injunction request seeks more spill over the dams and
increased river flow through Columbia-Snake River reservoirs to
help juvenile salmon migrate to the ocean. Science shows that
the quicker young salmon make it through the heavily dammed
river system, the higher their survival rate. But the Bush
administration’s salmon plan (also called a Biological Opinion,
or “BiOp”) released earlier this year rolls back – and even
eliminates – some of the key protections ordered by the court in
the past. Those court-ordered protections contributed to 2008’s
improved returns.

According to the Fish Passage Center, a government-funded,
independent science and data analysis agency that monitors
Columbia-Snake River salmon and steelhead, this year’s improved
returns are likely the result of more water left in the river
and the spilling of additional water over dams in 2006 when the
now-returning fish were migrating to the ocean as young salmon.
Judge Redden court-ordered those in-river improvements after
conservationists and fishermen fought to have them instituted –
over the vehement objections of federal agencies. Fishermen are
hailing the so-called “Redden effect” as an important tool for
keeping and creating sustainable jobs in the region until a
scientifically-sound, legally-valid salmon plan is in place.

This June, the State of Oregon, fishing and conservation groups
filed litigation against the Bush administration’s May 2008
salmon plan for violating the Endangered Species Act and the
Clean Water Act. Courts have already invalidated three prior
federal plans. On January 16, 2009, Judge Redden will hear oral
arguments on the merits of the case. The injunction requested
today is unlikely to be addressed until after the court rules on
the merits. Any ruling on the proposed injunction would be made
sometime after mid-February 2009.