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The three-dimensional Atlantis model can represent physical, chemical and biological processes and can incorporate direct human involvement, such as fisheries management, habitat improvements and economic outcomes. It has been used to study the food web to determine whether salmon in Puget Sound are more threatened by predators or by the lack of a stable food supply and to evaluate specific recovery actions to help the endangered Southern Resident killer whales.

Researchers are compiling a strategic list of scientific uncertainties related to Puget Sound recovery. The list will be used to prioritize future funding and research to address critical knowledge gaps about the ecosystem.

Chronic stress from lack of oxygen can make aquatic organisms more vulnerable to disease, pollution, or predation. Low oxygen can also result in reduced habitat for some species. Aquatic species may escape, acclimate, adapt, or die with exposure.

Estuaries around the world including Puget Sound perform an amazing feat of continuous water mixing called estuarine exchange flow. 

Like the air we breathe, oxygen that is dissolved in the water is critical for aquatic life. When dissolved oxygen is low, fish and other aquatic organisms may not be able to survive. 

Nitrogen is a chemical element that is essential for the growth of all life on earth. But too much nitrogen can lead to low dissolved oxygen and other problems such as toxic algal blooms that can harm or kill aquatic organisms. 

The following fact sheet provides an overview of low oxygen conditions in Puget Sound. It addresses some of the related causes and concerns that have been identified by scientists in the region. The overview was prepared in conjunction with a series of workshops on hypoxia and nutrient pollution presented by the University of Washington Puget Sound Institute. 

In many parts of Puget Sound, hypoxic waters are thought to be at least in part due to overgrowth of microscopic algae, which is triggered by excess nitrogen. That means it’s important to understand the dynamics of primary productivity – the rate at which those microscopic algae, known as phytoplankton, produce organic matter through photosynthesis and in this way provide the base of the food web. Researchers are investigating different types of phytoplankton and rates of primary productivity throughout the Salish Sea, and seeking to understand how primary productivity is likely to change as climate change alters patterns of coastal upwelling and freshwater flow into the Sound.

How do marine sediments affect oxygen and nutrient levels in the water?

Treaty rights are critical to the sovereignity of Puget Sound area Tribes and are deeply connected to natural resource management. Five landmark treaties in our region were signed during a three-year period from 1854 to 1856 and continue to drive policy to this day.  

The search goes on for a set of definitions and thresholds to represent low-oxygen concentrations that threaten various aquatic creatures. Over the years, ecologists have relocated, reshaped and revised the word “hypoxia” to describe these conditions. In part four of our series "Oxygen for life" we look at how scientists determine whether oxygen levels are low enough to be considered harmful to sea life. 

Scientists are reporting a decline in oxygen-rich waters throughout the world. Causes for the decline vary from place to place but may involve climate change and increasing discharges of tainted water. In Puget Sound, low oxygen levels can occur naturally or due to eutrophication from human-caused pollution. In this five-part series, we describe the critical nature of oxygen to Puget Sound sea life. Scientists are finding that changes in oxygen levels can lead to physiological adjustments, shifts in predator-prey relationships and other repercussions throughout the food web.

As observed in Hood Canal, low-oxygen conditions can upend the lives of Dungeness crabs trying to stay alive. Levels of dissolved oxygen can alter predator-prey relationships for a multitude of species, affecting populations throughout the food web. Part two of our series "Oxygen for life" examines a crab case study.

In time, lower dissolved oxygen worsened by climate change could increase the abundance of rare species in Puget Sound while putting populations of more common species into a tailspin. Part three of our series "Oxygen for life" looks at how warmer waters will gradually make it harder for many sea creatures to breathe. 

While a scarcity of Chinook salmon and other environmental factors may be pushing the Southern Resident killer whales toward extinction, a new genetics study has revealed that inbreeding has been exerting a powerful, overriding influence upon the small, genetically isolated population.

A 2023 paper in the journal Marine Ecology Progress Series examines seabird reproductive and dietary response to a severe marine heat wave affecting the California Current ecosystem from 2014 to 2016. The study involved rhinoceros auklet colonies on Destruction Island (California Current) and Protection Island (Salish Sea). The paper's first author Eric Wagner describes some of the findings from the study in this informal summary.

Each year, the Puget Sound Ecosystem Monitoring Program (PSEMP) releases a Puget Sound Marine Waters Overview, a report combining a wealth of data from numerous comprehensive environmental monitoring programs. The latest report provides an overview of marine conditions in 2021 and represents the collective effort of 76 contributors from federal, tribal, state, and local agencies, academia, nonprofits, and private and volunteer groups. 

Biologists are intrigued by the prospect of island-hopping cougars in the Salish Sea. Could swimming ability lead to improved genetic diversity among the big cats?

The Washington State Department of Ecology has reached one hundred Eyes Over Puget Sound reports. Since 2011, Ecology has provided aerial observations and documented visible features at the surface of Puget Sound from a floatplane. This unique perspective from the air featured Puget Sound's natural beauty, its oceanographic complexity, and its ecological treasures. It also raised awareness of the challenges that the water body is facing today. Our image-rich documentation of known eutrophication indicators ranges from algal and Noctiluca blooms to macroalgae, jellyfish, and human stressors. It provides a visually captivating time-capsule of issues facing Puget Sound. The report is rich in educational and outreach material, inspired numerous news reports, and drew academic and public attention during the period of marine heat wave of the north Pacific, The Blob.

Environmental reporter Christopher Dunagan remembers the life and influence of pioneering orca researcher Ken Balcomb.  

The report comes after a third year of La Nina conditions. Weak upwelling off the coast and low river flows of major rivers meant less cold, nutrient-rich, upwelled water was being entrained into Puget Sound in late summer and fall. Water conditions in Puget Sound in October were generally expected while Willapa Bay and Grays Harbor were both unusually warm and salty. Smoky air restricted our flight to Southern Puget and Central Sound where we saw blooms in terminal bays as well as patches of jellyfish. Sediment in Commencement Bay and along shorelines in Totten Inlet was unusual for a dry fall. A healthy foodweb has at its base a balance of nutrients. Explore what we found over the period of two decades of monitoring.

How do excess nutrients trigger low oxygen conditions in Puget Sound and what do those conditions mean for the species that live here?

Diverse communities of microscopic organisms called phytoplankton make up the base of the aquatic food web. In that role, they are essential to the tiny animals that eat them, but phytoplankton are not dependent on others. Thanks to chlorophyl, these tiny organisms can generate their own energy from nutrients and sunlight. Despite their critical importance to a great diversity of sea life in Puget Sound, phytoplankton can also contribute to low-oxygen conditions, and some can be harmful in other ways.

In a new series we are calling Ask a Scientist we interview local researchers to get their thoughts on some of the important but lesser-known scientific facts about the Puget Sound ecosystem. Today, we speak with University of Washington oceanographer Parker MacCready about Puget Sound’s “underwater Amazon” and why it has profound implications for Puget Sound science and policy. It all begins, he says, with the mixing of fresh and salt water and something called the estuarine exchange flow.

Fall’s chill is in the air (finally!), leaves are turning colors, and skeletons and spider webs are popping up in yards all over town. Meanwhile, under the mud of Puget Sound, there’s a strange critter that stays in its ethereal costume all year long – the burrowing ghost shrimp.