High levels of mercury and other toxic chemicals are showing up in seemingly remote and pristine parts of the Puget Sound watershed, the result of atmospheric deposition. Scientists talk about a “dome” of pollution hanging over urban areas, leading to a never-ending cycle of persistent compounds working their way through the air, onto the land and into the water.

Scientists are still trying to understand what caused the deaths of thousands of rhinoceros auklets in the Salish Sea in 2016. Some studies point to disease as a central factor in that incident and potentially other large seabird die-offs along the coast. That is prompting a deeper look at what makes these birds sick, and how local populations are faring. We followed a group of researchers as they gave a health checkup to a breeding colony of rhinoceros auklets on Protection Island.

They rival tropical forests in their richness and diversity, but Puget Sound's kelp beds have declined steeply in recent decades. Scientists are just starting to understand the extent of these losses. What they are finding is bringing kelp to the forefront of Puget Sound's environmental concerns.

A 2019 story map produced by the University of Washington Puget Sound Institute in collaboration with the Washington Department of Fish and Wildlife shows how shoreline armoring can often be replaced by softer, shore-friendly features.

Scientists believe that herring have been a staple of Salish Sea food and culture since humans first arrived here at least 12,500 years ago. That importance has continued into modern times, even as herring numbers have declined in parts of the region. 

Pigeon guillemots have attracted relatively little scientific attention compared to other seabirds in Puget Sound. That may be because their population is generally stable, but a group of citizen scientists is helping to put guillemots on the conservation radar. They hope the birds can be used as an indicator of Puget Sound health.

The Washington Department of Natural Resources is studying new ways of increasing ecologically important eelgrass habitat in Puget Sound. It is part of the state's effort to boost eelgrass 20% Sound-wide by 2020. So far, recovery of the species has fallen short of that goal, but transplanting efforts are showing promise. 

Each winter and spring, researchers survey the sometimes spectacular spawning events of Puget Sound's Pacific herring. They have found wide swings in the fish's population and an overall decline in herring numbers since the 1970s, but little is known about the cause or what this might mean for the health of the food web. We spent a day with a biologist spotting herring eggs and considering the future of one of our region's most ecologically and culturally important fish species. 

The Toxics in Fish Implementation Strategy is a recovery plan that will be used to guide funding and activities to reduce the impacts of toxics contaminants on marine fish and the humans that consume them. The plan is scheduled to be completed in 2019.

Understanding the social networks and family bonds of Puget Sound's southern resident orcas may be critical to keeping the endangered whales from extinction. A healthy population is about more than numbers, scientists say. It's about connections.

This three-part series explores opportunities and challenges of using medical interventions to save Puget Sound's southern resident orcas from extinction. Part 1 looks at how scientists might treat endangered southern resident orcas that face starvation and risks of disease; Part 2 considers how veterinarians have intervened with other animals in the wild, and how this might apply to orcas in Puget Sound; and Part 3 explores a federally approved vaccination program designed to ward of a deadly virus among endangered Hawaiian monk seals.

Puget Sound’s only native oysters were nearly wiped out in the 19th century from overharvesting. Now a network of scientists and advocates is working to restore them to their historical and cultural prominence.

For critically endangered animal populations, experts worry that a highly infectious disease could be the final nail in the coffin, forcing the species into extinction. That’s one reason why federal authorities approved the development and deployment of a new vaccine to ward off the deadly morbillivirus among Hawaiian monk seals. The vaccination program raises the possibility of using vaccines to prevent disease among Puget Sound's southern resident killer whales, but no specific steps have been taken so far.

As the plight of Puget Sound’s southern resident orcas becomes increasingly desperate, with the population dropping from 98 to 75 in just 22 years, scientists are weighing the options of medical intervention. In part two of our two-part series The Orca Docs we look at how veterinarians have intervened with other animals in the wild, and how this might apply to the situation here in Puget Sound. [Part one, "When should medical experts intervene to save a killer whale?" is also available.]

The death of a young female orca in September has sparked a discussion of how and whether scientists should step in with medical care for distressed animals in the wild. Medical intervention has become routine for some endangered mammals, but scientists say Puget Sound’s resident orcas present a series of unique challenges and ethical questions. In part one of our two-part series The Orca Docs we look at how scientists are preparing to treat endangered southern resident orcas that face starvation and risks of disease.

Can scientists bring back the lost tidal forests of Puget Sound? It could take generations, but restoring this rare habitat will pay big dividends for Puget Sound’s salmon.   

A 2018 report published by Washington Department of Fish and Wildlife and Washington Department of Natural Resources describes a regional strategy to reduce shoreline armoring in the Puget Sound region.

The federal Clean Water Act of 1972 was designed as a logical step-by-step approach to clean up the nation's waterways. Most people acknowledge that the law has been effective in reducing pollution, but industrial and environment groups tend to be on opposite sides when discussing whether regulations and permits adequately protect water quality. These 10 elements of the Clean Water Act (CWA) focus on how the law applies to Puget Sound.

With a population growth of about 10 percent per year in inland waters, harbor porpoises are having an undetermined but growing effect on food dynamics in Puget Sound.

As critically important eelgrass declines in some parts of Puget Sound, scientists are trying to plant more of it. The health of the ecosystem may be riding on their efforts, but what they are finding is something that farmers have known for thousands of years: Getting something to grow may be harder than you think.

Recent images of a mother orca appearing to grieve for her dead calf have brought worldwide attention to the plight of Puget Sound’s endangered Southern Resident orcas. As orca numbers decline, we look at how the effects of toxic chemicals on the whales are magnified even as the residents slowly starve from a general lack of Chinook salmon, their chief source of food. 

An intensive research program in the U.S. and Canada is studying why so few salmon in the Salish Sea are returning home to spawn. It is uncovering a complex web of problems involving predators, prey and other factors that put salmon at risk as they migrate to the ocean. We present a four-part series on the Salish Sea Marine Survival Project, including new findings presented at the 2018 Salish Sea Ecosystem Conference last spring in Seattle.

Chemicals, disease and other stressors can increase a salmon's chance of being eaten or reduce its ability to catch food. We wrap up our series on the Salish Sea Marine Survival Project with a look at some of the lesser-known, but still significant factors contributing to salmon declines in the Salish Sea.

A recent influx of anchovies into Puget Sound may have saved some steelhead from predators, but researchers seek more evidence to prove the connection. Our series on the Salish Sea Marine Survival Project continues with a look at these and other potential impacts from predators on the region's salmon and steelhead.

Getting bigger faster can help save juvenile Chinook salmon from a gauntlet of hungry predators ranging from birds and marine mammals to larger fish. We continue our series on the Salish Sea Marine Survival Project with a look at what helps salmon grow and prepare for life in the open ocean. 

An intensive research program in the U.S. and Canada is studying why so few salmon in the Salish Sea are returning home to spawn. They are uncovering a complex web of problems involving predators, prey and other factors that put salmon at risk as they migrate to the ocean. We begin a four-part series on the Salish Sea Marine Survival Project, including new findings presented at the 2018 Salish Sea Ecosystem Conference last spring in Seattle. 

A high-profile salmon escape led to a ban on salmon farms in Washington earlier this year. But just across the border, scientists say salmon farms in British Columbia expose migrating fish from Puget Sound to potential maladies like parasites, bacteria and dangerous viruses. They say simply getting rid of salmon farms in Washington does not put the potential impacts to rest. 

As the region's population grows, scientists say we can expect to see increasing amounts of nitrogen and other elements flowing into Puget Sound. Known as “nutrients” these elements are naturally occurring and even necessary for life, but officials worry that nutrients from wastewater and other human sources are tipping the balance. That could mean big problems for fish and other marine life, gradually depleting the water of oxygen and altering the food web.

High amounts of elements such as nitrogen can cause blooms of phytoplankton that sometimes trigger perturbations throughout the food web. This occurs most often in the spring and summer after the long, dark, cloudy days of winter begin to fade.

The amount of oxygen in the Salish Sea is dependent on water circulation which distributes chemical elements such as nitrogen through the system.

As wildlife managers work to recover Puget Sound’s diminished Chinook population, a proposed white paper is expected to review the impacts of some of the salmon's chief predators. The study would include a section on potential management of seals and sea lions, prompting open discussion of a long taboo subject: Could officials seek to revise the Marine Mammal Protection Act — or even conduct lethal or non-lethal removal of seals and sea lions in some cases? Such actions are hypothetical, but we look at some of the ongoing discussions around the issue as prompted by a new resolution from the Puget Sound Leadership Council. 

Researchers are trying to determine which chemicals in stormwater are contributing to the deaths of large numbers of coho salmon in Puget Sound. It has prompted a larger question: What exactly is in stormwater, anyway?

Increased consumption of Chinook salmon by seals and sea lions in the Salish Sea “could be masking the success of coastwide salmon recovery efforts,” according to a new study published in the journal Scientific Reports. Endangered resident orcas are said to be declining in part due to a lack of available Chinook, the orcas' preferred prey.

Climate change could cause sea levels to rise more than four feet in some parts of Puget Sound, leaving shoreline residents with some tough decisions. Experts say fighting the waves with conventional seawalls may not be the answer.

A new study shows a surprising decline in some toxic chemicals in Puget Sound fish, while levels of PCBs increased in some cases. Scientists say the study shows that banning toxic chemicals can work, but old contaminants remain a challenge as they continue to wash into Puget Sound.

Toxic chemicals have been showing up in Puget Sound fish for more than a century, but consistent testing over the past 30 years has helped to reveal some unusual patterns of pollution.

In recent decades, hundreds of millions of dollars have been spent to restore habitat for Puget Sound salmon. In this article, we look at how scientists are gauging their progress. Are environmental conditions improving or getting worse? The answer may depend on where you look and who you ask.

Scientists want to know why eelgrass is on the decline in some areas of Puget Sound and not others. The answer will affect future strategies for protecting one of the ecosystem’s most critical saltwater plants.

When rivers spill into Puget Sound, they provide some of the most productive habitat in the ecosystem. The ebb and flow of the tides creates a perfect mix of fresh and salt water critical for young salmon. But over the past 100 years, the region’s tidal wetlands have declined by more than 75%. Now a coalition of state and federal agencies has a plan to bring them back.

The state of Washington estimates that the Puget Sound area will grow by more than 1.5 million residents within the next two decades. That is expected to have profound effects on the environment as more and more people move to undeveloped areas. The race is on to protect this critical rural habitat, but planners say what happens in the cities may be just as important.

A new approach to flood control is taking hold across Puget Sound. Rivers, scientists say, can be contained by setting them free. Conservationists hope this is good news for salmon recovery.

As threatened Chinook populations in Puget Sound continue to lose ground, the state is looking to new strategies to reverse the trend. In the Skagit watershed, the scientists — and the fish — are among those leading the way. 

After a long struggle with pollution, Drayton Harbor has reopened to year-round commercial oyster harvesting for the first time in 22 years. Here’s how the community cleaned up its act, potentially showing the way for shellfish recovery throughout Puget Sound.

A new study shows that increased populations of seals and sea lions are eating far more of Puget Sound’s threatened chinook than previously known, potentially hampering recovery efforts for both salmon and endangered killer whales. 

Many groups have been formed around the goal of saving salmon, but few people talk about a concerted effort to save microscopic creatures. Whether or not a pro-bug movement catches on, future strategies to save salmon are likely to incorporate ideas for restoring streambound creatures known as benthic invertebrates.

A "learn and adjust" strategy known as adaptive management plays a central role in state and federal Puget Sound recovery efforts. It is an approach that is gaining traction for ecosystem management worldwide. A December 2016 article from the Puget Sound Institute provides an overview of the concept and how it is being applied locally.