Keywords: Species and food webs, Invertebrates, Zooplankton, Salmonids, Marine heat waves, Phytoplankton, Monitoring

Zooplankton are critical to the marine food web, but until recently there have been few surveys of the zooplankton community in Puget Sound. Ongoing monitoring is now revealing a system full of complexity and surprises. The following article was commissioned by the Habitat Strategic Initiative Lead (HSIL), a cross-agency team co-led by the Washington Departments of Fish and Wildlife and Natural Resources.

In 2014, Long Live the Kings, a non-profit organization devoted to Pacific salmon restoration and recovery, received a grant to begin what biologists hoped would be a long-term zooplankton monitoring project in Puget Sound. The project would involve tribal governments, universities, state agencies, federal agencies, and other non-profits. “It was quite the undertaking, given that there are so many partners and stakeholders,” says Julie Keister, a biologist at NOAA who now helps oversee the program. “It was a reflection not just of how important zooplankton are to Puget Sound, but also how not a lot was known about them.”

Puget Sound Zooplankton Monitoring Program

The Puget Sound-Wide Zooplankton Monitoring Program was established as part of the Salish Sea Marine Survival Project in 2014 to monitor changes in zooplankton communities of Puget Sound. The program involves 12 partners from tribal, county, state, federal, academic, and non-profit entities that collaborate to sample the zooplankton community regularly at 16 sites throughout Puget Sound. The program’s long-term data collection and monitoring allows scientists and managers to track ecosystem health and understand the primary food source for juvenile salmon, herring, and other fish in Puget Sound. With the help of multiple funding sources and partner cooperation, the zooplankton monitoring program has run continuously from 2014-2022, with a brief break in 2020 due to the COVID-19 pandemic.

Additional information for the zooplankton monitoring projects funded in 2016 and 2020 is available on the Puget Sound National Estuary Program website.

Young salmon including Chinook feed on microscopic zooplankton like krill and copepods seen on the right. Photos: (Left) Roger Tabor/USFWS (CC BY-NC 2.0); (right) Jeff Napp/NOAA (CC BY 2.0)

Plankton form the sprawling base of every conventional marine food web. They are divided into two general types. Phytoplankton are, in essence, plants; they are at the very bottom of the food web, or the lowest trophic level. Zooplankton, as organisms that eat phytoplankton, sit just above them. Zooplankton can be small animals, like copepods; or younger life stages of what will eventually grow to become larger, more visible animals like crab or shellfish larvae. As such, most zooplankton are microscopic, but some, like jellyfish, are so large that they can be seen quite easily.

Three side by side images of copepods, jellyfish, and crab larvae

Most zooplankton are tiny, microscopic animals like copepods (left) but some, including jellyfish (middle), are large enough to be easily seen. Others may be early life stages of animals that grow larger like Dungeness crab zoea (larvae) seen on the right. Photos: (Left) NOAA; (middle) M.Evans (public domain); (right) Don Rothaus/WDFW

The word plankton comes from planktos, which is Greek for “wanderer”; and plankton in general are marked by a certain tendency to drift, or wander, going as they do largely where the tides or currents take them. But rather than being mere passive drifters, zooplankton are particular organisms in their own right. Many can swim up and down in the water to help control the direction they drift. Some do well in warmer water, and others thrive in cold. Some are large and fatty (relatively speaking), while others are smaller and comparatively less nutritious.

In 2015, the first year of The Blob, rather than becoming a zooplankton desert, Puget Sound was full of copepods and other organisms.

Where zooplankton become vital is that they themselves are then eaten by a host of species, including some that humans care a lot about, like young salmon. The purpose of the monitoring project, then, was to see how the zooplankton’s ups and downs played out in the more or less confined spaces of Puget Sound. The approach would be straightforward conceptually if not logistically. Every year, teams of biologists would do biweekly zooplankton surveys from the spring through the fall, at points from the San Juans down to South Sound. By lowering a net to within a few meters of the bottom and drawing it to the surface, they would be able to characterize Puget Sound’s zooplankton community, seeing how it varied in space and time.

Puget Sound recovery strategic initiatives

This article was commissioned by the Habitat Strategic Initiative Lead (HSIL), a cross-agency team co-led by the Washington Departments of Fish and Wildlife and Natural Resources, as part of a grant to the Puget Sound Institute to synthesize and communicate on 100 grant awards made by the HSIL between 2016-2020 with EPA Puget Sound Geographic Program funds.

About HSIL

The 2012-2013 Action Agenda for Puget Sound developed by the Puget Sound Partnership established three initiatives to tackle multiple issues critical to Puget Sound recovery:

  • habitat protection and restoration
  • shellfish bed protection and recovery
  • stormwater pollution prevention.

To manage this effort, agency and institutional partners assembled into three Strategic Initiative Lead (SIL) teams, charged with bringing people and ideas together to improve the water, habitat, and communities. Read more about the Puget Sound Recovery Program.

The role of HSIL is to implement plans that improve the health of the rivers, forests, shorelines, and estuaries that make up Puget Sound. The Puget Sound Zooplankton Monitoring Program was one of several projects to receive HSIL funding.

The monitoring project is ongoing, but that was not always assured. After the initial grant to Long Live the Kings ended in 2016, it was not at all clear the program would survive. That it does is thanks to funding from the Environmental Protection Agency distributed through a consortium of state agencies known as the Habitat Strategic Initiative Lead. Funds from that program allowed the project to transition to the Washington Department of Fish and Wildlife (WDFW), which will steward it going forward. And in April, some results of the survey work were published in the journal Progress in Oceanography. There, the authors took advantage of their dataset to see how Puget Sound’s zooplankton community responded to The Blob, as the large marine heatwave that affected the northeastern Pacific from 2014 through 2016 has come to be called.

“It appears that a lot of what is happening in Puget Sound is affected by local processes, rather than necessarily mirroring what’s happening on the coast. That was our really big takeaway.” -- Amanda Winans, UW School of Oceanography 

The Blob was a massive event. At its peak, more than one million square miles of the north Pacific were affected, and to a depth of up to three hundred feet. Its ecological effects were profound and are still being investigated. But with such a wide area to consider, scientists sometimes have to rely on a kind of geographic shorthand. “Most efforts to study and characterize The Blob’s effects in the California Current system have been on the outer coast,” Keister says. “What happens out there obviously influences what happens in the inland waters, but these data gave us a chance to focus more on Puget Sound and the Salish Sea.” 

For their paper, the authors focused on 2015 and 2016, when The Blob most greatly affected the inland waters, and considered the regional zooplankton community at the intersection of time, space, and climate. What they found was a marine space full of complexity and surprises. Levels of chlorophyll, for instance—an indicator of phytoplankton levels, or how much food was available to zooplankton—did not show a consistent relationship with temperature, being fairly high in 2015 before becoming patchier in 2016.

Where zooplankton were concerned, there were anomalously high increases in their biomass across the entire Puget Sound. In 2015, the first year of The Blob, “It was across the board,” says Amanda Winans, a research scientist in the University of Washington School of Oceanography who was lead author on the paper. Rather than becoming a zooplankton desert, Puget Sound was full of copepods and other organisms. These increases persisted through 2017 in southern Puget Sound sites, but not in northern sites in the Strait of Juan de Fuca. Copepod species in Puget Sound that favor warm water did well throughout, while species that prefer cooler water, and thus tend to be larger, did not. (“That, at least, was not a big surprise,” Winans says.)

“This increase in zooplankton contrasted with reports of many coastal populations, especially in the [California Current System] where total biomass generally decreased during the [marine heatwave],” the authors wrote. Why the patterns in Puget Sound differed from those on the outer coast is not entirely clear, although there are some clues. The Salish Sea Model, for instance, suggested that freshwater inputs into Puget Sound were much higher in 2015, which in turn increased the exchange flow and brought more nutrients into the inland waters from the outer coast, leading to greater amounts of phytoplankton. Additionally, the warmer temperatures experienced in Puget Sound during The Blob may have spurred growth for resident zooplankton, which were able to gorge on those phytoplankton.

“It appears that a lot of what is happening in Puget Sound is affected by local processes, rather than necessarily mirroring what’s happening on the coast,” Winans says. “That was our really big takeaway.”

The work for the recent paper ties in with a study Keister published last fall, looking for links between climate, zooplankton dynamics, and survival patterns of Chinook and coho salmon in the Strait of Juan de Fuca, which is at the northern terminus of Puget Sound. In that study, she and her co-authors showed that zooplankton communities had strong seasonal patterns, alternating between species that were present in Puget Sound (which tended to be smaller) and others brought in from the outer coast (which tended to be larger). Juvenile salmon tended to do better when zooplankton communities were dominated by outer coast species—precisely the kind that did not fare so well during The Blob.

“People had been making assumptions about how Puget Sound food webs would operate based on coastal observations,” she says. “This study shows that Puget Sound is actually quite different.” Continuing the zooplankton survey for years to come will be crucial in this regard; that it is now housed in WDFW could help it stretch on indefinitely. “That’s one of the key takeaways from this work,” Keister says. “To understand Puget Sound, you have to study Puget Sound.”


Food web and climate monitoring supported by the Habitat Strategic Initiative Lead

Ecosystem health depends upon the vitality of food web interactions and resilience to stressors like ocean acidification. The Puget Sound-Wide Zooplankton Monitoring Program was one of several monitoring efforts related to the marine food web and associated climate stressors to receive EPA Puget Sound Geographic Program funding through the Habitat Strategic Initiative Lead. Other projects are described below.  

Ocean acidification hotspots and sources of shellfish resilience

Following a 2014 study that showed eelgrass photosynthesis pulled enough carbon dioxide out of the water to  increase its pH, the Washington Department of Natural Resources wanted to start exploring eelgrass’ potential to mitigate the impacts of ocean acidification on shellfish. A key element of this work was the 2015 establishment of an Acidification Nearshore Monitoring Network (ANeMoNe) where autonomous water quality sensors measure pH, salinity, temperature, dissolved oxygen, and chlorophyll concentrations at 10-minute intervals year-round.  ANeMoNe started with eight intertidal sites, and by 2023 had expanded to 13. At each site. sensors are deployed in eelgrass beds and in adjacent unvegetated areas. Monitoring data revealed differences in chemical composition and temperature among sites, suggesting there may be microclimates within and around Puget Sound that could serve as refugia as climate change continues to alter the environment at large. The grant supported a series of experiments about the effects of eelgrass on shellfish recruitment and growth. Preliminary results indicate eelgrass restoration has potential as an ocean acidification remediation tool. When eelgrass is most actively growing, in the spring and summer, photosynthesis has detectable effects on pH at local scales. This effect occurred during the time of year when sensitive bivalve larvae are most common in Puget Sound. 

Add acidification parameters to Ecology monitoring network

Grant funding allowed the Washington Department of Ecology to add two new measures to their marine monitoring program: total alkalinity (TA) and dissolved inorganic carbon (DIC). Although pH had long been a parameter measured as part of Ecology’s monitoring program, these two new parameters were needed to understand more about carbon dynamics and acidification in marine waters. TA and DIC measurements are used to calculate the Omega (Ω) value, or aragonite (CaCO3) saturation state, of a water sample. This parameter has emerged through laboratory and field studies as a strong indicator of ocean acidification. As CO2 rises, Ω declines. Ω values above 1 imply that waters are abundant in stable CaCO3, which juvenile shellfish can use to build shells. Ω values below 1 cause CaCO3 to start dissolving. This makes it harder for juvenile shellfish to form shells. The OMEGA project, as it has come to be called, has begun to address knowledge gaps about ocean acidification in nearshore waters. Initial results from the first two years of monitoring showed promise for this program’s ability to document long-term changes in water chemistry resulting from anthropogenic carbon emissions. In 2019, Ecology requested and received an appropriation from the Legislature to make the new parameters a permanent part of the marine monitoring program. 

Investigation of nutrients and phytoplankton in Admiralty Inlet and Northern Hood Canal

This project added phytoplankton and nutrient monitoring to two existing zooplankton monitoring program sampling stations —Admiralty Inlet and Hood Canal — in 2021. By coupling zooplankton data with phytoplankton and nutrient data, scientists will gain a more complete understanding of the environment that juvenile and adult salmon encounter in their migrations to and from their natal streams. The result will be a deeper understanding of the base of the food web and the incidence of harmful algal blooms (HABs), which can impact salmon survival. Seasonal phytoplankton and nutrient patterns were observed including the presence of species potentially harmful to salmon and those which produce biotoxins. These species included the diatom Chaetoceros convolutes in concentrations that have been known to kill salmon on fish farms. Other notable findings were that the spring phytoplankton bloom in Hood Canal started earlier than at Admiralty Inlet and that nutrients became depleted at the surface in the summer in Hood Canal but not at Admiralty Inlet.

Assessing Pacific Sand Lance subtidal habitats and biomass in regard to salmon foraging in the San Juan archipelago

The Pacific sand lance is a critical forage fish for many organisms in Puget Sound and the Salish Sea. This project performed gut analyses on 109 Chinook and coho salmon stomach samples harvested from San Juan County. The goal was to determine the importance of sand lance in salmon diets and additionally identify potential sand lance habitats. Recreational fishers and charter boats provided the Chinook and coho stomach samples and harvest location data. Moss Landing Marine Laboratories and project partners then compared the location data of salmon with sand lance gut contents to potential and known sand lance sub-tidal habitats. Biologists identified over 275 bedforms in the Salish Sea, and classified their potential for sand lance; 106 of those sites were rated as having good or better potential for sand lance. This study began development of a stomach content database for San Juan County and sets the stage for using developed methodologies to find more preferred foraging habitats of Chinook and other salmon.

Growth and life history strategies of Salish Sea Chinook salmon as they relate to marine survival, habitat condition, and population recovery

As people try to help Chinook salmon populations recover throughout Puget Sound, understanding all the ways that young fish use habitats is critical to help to focus restoration efforts. This project linked biotic and abiotic factors to life history expression, considering such factors as Chinook population size, a site’s distance from the estuary, the amount of riverine and estuarine habitat available, as well as contaminant and parasitic levels. Results from this research showed that juvenile Chinook life history success is not equal among the populations examined in Western Washington. Estuaries with more area in a natural state generally had more juvenile salmon use them. 

This article has been funded wholly or in part by the United States Environmental Protection Agency under assistance agreement PC-01J22301 through the Washington Department of Fish and Wildlife. The contents of this document do not necessarily reflect the views and policies of the Environmental Protection Agency or the Washington Department of Fish and Wildlife, nor does mention of trade names or commercial products constitute endorsement or recommendation for use.


Aerial view of Interstate 5 stretching across a large area of land covered by brown flood waters from the Nooksack River in the foreground with mountains and Puget Sound in the distance and grey skies above.

All across the region, communities are finding that rising seas and rising rivers are two sides of the same coin. New research funded by the Environmental Protection Agency may help managers target their responses to climate-fueled flood risks in Puget Sound. The following article was commissioned by the Habitat Strategic Initiative Lead (HSIL), a cross-agency team co-led by the Washington Departments of Fish and Wildlife and Natural Resources.


A beaver sitting at the base of small tree on mud surrounded by green vegetation.

Beavers provide critical benefits for wetland ecosystems but can also alter the landscape in ways that are unpredictable for property owners and conservationists alike. New techniques are helping humans and beavers share the landscape with the goal of benefiting both parties. The following article was commissioned by the Habitat Strategic Initiative Lead (HSIL), a cross-agency team co-led by the Washington Departments of Fish and Wildlife and Natural Resources.

About the author: Eric Wagner writes about science and the environment from his home in Seattle, where he lives with his wife and daughter. His writing has appeared in Smithsonian, Orion, The Atlantic and High Country News, among other places. He is the author of "Penguins in the Desert" and co-author of "Once and Future River: Reclaiming the Duwamish." His most recent book is "After the Blast: The Ecological recovery of Mount St. Helens," published earlier this year by University of Washington Press. He holds a PhD in Biology from the University of Washington.