Encyclopedia of Puget Sound

Does Puget Sound need a diet? Concerns grow over nutrients

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.

A milky, turquoise, phytoplankton bloom in Hood Canal visible from space. Natural color MODIS image from Landsat 8 acquired July 24, 2016. Photo: NASA Earth Observatory https://earthobservatory.nasa.gov/NaturalHazards/view.php?id=88454
A milky, turquoise, phytoplankton bloom in Hood Canal visible from space. Natural color MODIS image from Landsat 8 acquired July 24, 2016. Photo: NASA Earth Observatory https://earthobservatory.nasa.gov/NaturalHazards/view.php?id=88454

Key takeaways

  • Scientists are concerned that nutrients from wastewater and other sources are gradually altering the chemistry of Puget Sound.
  • Nitrogen and phosphorous are naturally occurring nutrients that are necessary for life, but in excess amounts can cause increasing algal blooms and changes in the food web. This can lead to lower oxygen in the water and other serious problems for the ecosystem. 
  • Computer models suggest that natural sources such as ocean currents contribute about two thirds of the nutrients in the waterway, but human sources may be upsetting the natural balance, especially in poorly-mixed embayments. 
  • Human sources of nutrients from within the Puget Sound basin typically include wastewater from sewage treatment plants, runoff from agriculture and lawns and gardens, leaky septic tanks, stormwater and atmospheric deposition via the burning of fossil fuels and organic matter. 

While assessing the spread of an invasive sea squirt along the bottom of Hood Canal, divers for the Skokomish Tribe came upon a fluffy mass of white stuff that loomed like a ghost in the murky depths of Lynch Cove.

“It was our last dive of the day,” recalled shellfish biologist Chris Whitehead, working alongside another tribal diver when they made the surprising discovery in 2006. “We dropped down and were about midway through the water when we saw something white and wavy.”

The white flocculent, which seemed to glow in the dark, stretched up from the bottom, Whitehead said. The area looked to be covered with dirty snow as far as they could see in the murky water. Not one living creature was anywhere to be found. Instead, the mucky bottom was strewn with dead Dungeness crabs, small fish and unrecognizable remains of other organisms.

“We had no idea what this was,” Whitehead said. “It was an eerie feeling. We were in kind of a panic and really concerned. I had never seen anything like that.”

Later, biologists would identify the milky white substance as a bacteria, Beggiatoa, which grows in very-low-oxygen conditions among deposits of organic material. It turns out that the bacteria are fairly common, growing within the soft sediments of Puget Sound. What is unusual is for the bacteria to emerge from the sediments in billowy mats across the bottom, as the Skokomish divers discovered in 2006.

Since then, researchers have found similar, though less impressive, bacterial mats in other coves and inlets of Puget Sound where the water circulates slowly, contributing to deadly declines in dissolved oxygen.

Core sample from Hood Canal showing a cotton-like mat of Beggiatoa bacteria extending above the seafloor. Oct 2006. Photo: Matt Lonsdale
Core sample from Hood Canal showing a cotton-like mat of Beggiatoa bacteria extending above the seafloor. Oct 2006. Photo: Matt Lonsdale

Such areas of extremely low oxygen, sometimes referred to as “dead zones,” are related to excess nutrients, such as nitrogen and phosphorous, that over-feed a large variety of tiny plankton drifting through the water. Researchers are just beginning to understand the profound importance of a healthy planktonic community needed to support an abundance of life in Puget Sound — from microscopic algae right up to the top predators such as orcas. For life as we know it, adequate oxygen is a key to survival.

Experts, government officials and others are struggling to respond to the interrelated problems of excess nutrients, massive plankton blooms and deoxygenation — problems that are expected to increase with climate change and as greater numbers of people move into the Puget Sound region.

Puget Sound has always had areas of low oxygen, such as Hood Canal, with its relatively slow water circulation. Inflows from the Pacific Ocean also send massive amounts of naturally occurring nutrients throughout the Sound. According to Washington State Department of Ecology, computer models suggest that the Pacific Ocean contributes "two thirds or more," of all the nutrients in Puget Sound. However, scientists are worried that a rapidly increasing human population and other factors such as agricultural runoff are starting to tip the balance. How quickly that will happen — or whether it is already happening — is still under debate. But regulators are examining the possibilities and possible solutions.

Phytoplankton blooms

All living things require nutrients to survive, and natural sources of nutrients are abundant — from vegetation along streams to ocean waters that come into Puget Sound. But too much of a good thing is not good at all. Such is the case with excess nutrients from human sources, such as human waste from sewage-treatment plants and septic systems, fertilizers from farms and urban landscapes, animal waste from livestock and pets, and atmospheric deposition from the burning of fossil fuels and organic materials.

Nitrogen, which is found in all these sources, is the primary nutrient that drives the growth of phytoplankton in marine waters, such as Puget Sound. Phytoplankton are tiny organisms that contain chlorophyll. In the presence of sunlight, they can multiply into massive plankton blooms, which appear as colorful blotches of green, brown or orange when viewing Puget Sound from an airplane.

An algae bloom visible on the surface of Ostrich Bay in Bremerton, WA. August 28, 2017. Aerial Photo: Christopher Krembs, WA Ecology Eyes Over Puget Sound
An algae bloom visible on the surface of Ostrich Bay in Bremerton, WA. August 28, 2017. Aerial Photo: Christopher Krembs, WA Ecology Eyes Over Puget Sound

Phytoplankton blooms were once a serious problem on Lake Washington, leading to changes in the way cities and counties handle sewage discharge.

Learn more about: Cleaning up Lake Washington

Phytoplankton and the zooplankton that eat them eventually die. Their tiny bodies drift to the bottom, where they are broken down by bacteria that suck up the available oxygen during the process. The changes can have further wide-ranging effects, from disruption of the food web to harmful algal blooms and increasing ocean acidification.

Blame it on the nitrogen?

Excess nitrogen can be blamed, in part, for a variety of problems in Puget Sound:

  • Low-oxygen conditions, which can be harmful or lethal to fish and many bottom-dwelling animals, including crabs, shrimp and creatures that live within the sediments.
  • Food web changes, which result from a growth of plankton species that cannot be eaten by herring and other forage fish that serve as prey for salmon, birds and marine mammals.
  • Excessive plankton density, which can block sunlight and impair the growth of critical seaweed habitats and sometimes injure or kill fish and shellfish by clogging their gills.
  • Harmful algal blooms, such as those that produce paralytic shellfish poison and domoic acid, which can cause illness or death among people and animals exposed directly to the toxins or by eating shellfish that have become toxic.
  • Ocean acidification, which can impair shell formation among developing shellfish and crustaceans.

Low oxygen is one of the most obvious results of nutrient overload. At various times, oxygen levels have become dangerously low in many areas of Puget Sound. The most serious problems have been observed in southern Hood Canal and the numerous inlets south of the Tacoma Narrows Bridge. Washington Department of Ecology has identified water-quality violations related to low oxygen in 143 designated areas within 39 bays, inlets and open-water sectors throughout Puget Sound.

These localized areas in bays and inlets are designated as “impaired” water bodies. Under the federal Clean Water Act, the state Department of Ecology is authorized to improve these poor water conditions, starting with a cleanup plan. In addition to the 143 impaired water bodies, another 333 areas in 54 inlets are suspected of low-oxygen problems, but more study is needed for confirmation. [Related story: How the state assesses low oxygen conditions in Puget Sound.]

Some bays and inlets have naturally low oxygen conditions because of poor circulation, but human sources of nitrogen can exacerbate the problem, experts say. Over time, conditions are expected to get worse, according to computer models that assess factors such as the area’s growing population and the impacts of climate change.

State response

Ecology’s Dustin Bilhimer, who has worked on water-quality problems for 18 years, now faces the greatest challenge of his career: coordinating a response to the nutrient-plankton-oxygen problem. The effort, called the Puget Sound Nutrient Source Reduction Project, involves a wide variety of researchers as well as decision-makers, environmental groups and other “stakeholders.”

Understanding the problem with the help of an advanced computer simulation known as the Salish Sea Model is the first step in finding a solution, Bilhimer says, acknowledging that the need for a clear strategy has never been greater.

“We need to figure out the best way to get the right investments on the ground as quickly as possible,” Bilhimer said, noting that development of the computer model is beginning to reveal where nitrogen enters Puget Sound, how it gets pushed around by currents, how it feeds the plankton, and why low-oxygen problems appear.

Puget Sound is deep and wide; its circulation varies; and its biology is complex. Solutions will involve reducing human sources of nitrogen. But which ones and by how much? Those responsible for nitrogen releases — whether from sewage-treatment plants, septic systems or farms — are demanding assurance that money spent on improvements will make a difference.

“I am anxious and ready to get down and implement things,” Bilhimer said, “but if we don’t do this in a way that is technically and legally defensible, then we open ourselves up to not getting anything done.”

Legal challenge

Last October, an environmental group announced that Ecology has spent too much time on studies and not enough time on action. Northwest Environmental Advocates, based in Portland, Ore., petitioned the agency to immediately launch a cleanup effort — a process called a total maximum daily load study, or TMDL for short. Meanwhile, the group said Ecology should limit releases of nitrogen from sewage-treatment plants that discharge into Puget Sound.

“Ecology concluded well over a decade ago that nitrogen coming from permitted sewage-treatment systems is slowly killing Puget Sound, but it refuses to clamp down on the discharge permits until it has a cleanup plan in place,” said Nina Bell, executive director of the group. “The Catch-22 is that Ecology won’t issue a cleanup plan because it will force municipal dischargers to clean up their pollution.”

In an earlier petition filed in February 2017, Northwest Environmental Advocates asked the federal Environmental Protection Agency to remove Ecology’s jurisdiction over discharge permits for wastewater treatment plants and other facilities. Failure to regulate nitrogen pollution was the primary reason given by the group.

In a formal response issued in December, Ecology denied the NWEA’s petition for a TMDL, saying it does not yet have enough information to begin the process.

“Although Ecology has decided to deny your petition, we share many of your concerns regarding nutrient impacts in Puget Sound,” states the letter signed by Deputy Director Polly Zehm on behalf of Director Maia Bellon. “Further, Ecology agrees that Puget Sound is impaired by nutrient pollution and a TMDL may be necessary to address this impairment.

“However,” the letter says, “Ecology does not agree with your contention that we have all the data and analysis necessary to immediately and effectively develop a TMDL for nutrients in a system as complex and vast as Puget Sound.”

NWEA’s Nina Bell said the group is considering its next steps, but the battle is far from over.


Runoff of nutrients from farm fields is one of the primary sources of nutrients in many coastal waterbodies. Photo: Lynn Betts | USDA NRCS (CC BY 2.0) https://flic.kr/p/7NwA1n
Runoff from farm fields is one source of nitrogen affecting the health of coastal water bodies, including Puget Sound. Photo: Lynn Betts | USDA NRCS (CC BY 2.0) https://flic.kr/p/7NwA1n


The source of the problem

The average human body excretes about seven pounds of nitrogen per year — although this number varies greatly from one individual to the next, according to a study for the EPA. From the toilet, the nitrogen goes to the sewage-treatment plant or septic system.

Most sewage-treatment plants are not designed to remove nitrogen, although some nitrogen compounds are trapped in sludge and trucked away. Likewise, septic systems release nitrogen, and a portion can get into the groundwater that flows into nearby streams.

Some 87 sewage-treatment systems dump nitrogen-rich effluent directly into Puget Sound. These systems range from a tiny plant serving 140 people at Alderbrook Resort on Hood Canal to King County’s West Point Plant, where 1.3 million people send their nitrogen wastes.

In total, the 87 sewage-treatment plants release a daily average of about 38 tons of dissolved inorganic nitrogen into Puget Sound, according to a report from the Department of Ecology. Two-thirds of that total comes from the four largest plants: West Point in Seattle, King County South near Renton, Tacoma Central and Everett.

Meanwhile, all the rivers and streams together deliver about 32 tons of nitrogen into Puget Sound on an average day, according to the Ecology report. That includes human and natural sources spread across 54 major watersheds. About two-thirds of the total nitrogen comes from areas drained by five major rivers: the Snohomish, Skagit and Stillaguamish, all north of Seattle; the Puyallup in Tacoma; and the Nooksack near the Canadian border.

Human sources of nitrogen in the rivers include fertilizers from farms and effluent from septic systems. The natural sources include decomposing vegetation, nitrogen-releasing plants, and salmon that have spawned and died. For all of Puget Sound, human sources contribute about 2.6 times more nitrogen than natural sources in the watersheds.

Meanwhile, varying amounts of nitrogen creep into Puget Sound from the Pacific Ocean in a deep layer of water with a high salt concentration. Some of this nitrogen ultimately gets mixed into surface layers, where the greatest biological activity takes place.

Related story

Puget Sound circulation triggers low-oxygen conditions at different times and in different places

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

All this nitrogen — from both human and natural sources — has the potential to feed phytoplankton in the presence of sunlight, possibly triggering low-oxygen conditions. But this is where the complexity begins, because the timing and location of the nitrogen discharges into Puget Sound may be more important than the total amount of nitrogen.

A billion-dollar question

One possible answer to excess nitrogen in Puget Sound seems rather simple: Install equipment to remove nitrogen at all sewage-treatment plants that discharge effluent into Puget Sound. But with costs estimated in the billions of dollars, everyone wants to know how much good would come of that.

King County alone would face enormous financial hurdles, according to Chris Townsend, the county’s manager of environmental and community services. For one thing, the West Point treatment plant — the largest sewage facility in Puget Sound — has no room for expansion. A new plant would need to be built elsewhere to remove nitrogen or produce reclaimed water, he said.

“The Wastewater Division in King County is a water steward,” Townsend said. “We want to make sure we are treating the wastewater properly. But if we’re going to make huge investments, we had better have a good story about why that’s a good idea.”

Townsend noted that cleaning up stormwater was listed as Puget Sound’s highest priority by Puget Sound Partnership and other environmental agencies. King County is spending hundreds of millions of dollars to clean up its stormwater — including efforts to eliminate combined sewage overflows, in which raw sewage escapes into Puget Sound during heavy rainfalls.

It will be important to get the priorities straight, Townsend said, considering that local governments have limited financial resources.

King County’s newest sewage-treatment plant, the $1.86-billion Brightwater plant near Woodinville, serves nearly 200,000 people in North King and South Snohomish counties. The plant produces high-quality Class A water for a portion of its effluent. This reclaimed water could be used for irrigation or other non-drinking purposes. The problem, Townsend said, is the cost of building pipelines and finding end users to take the water, so most of the effluent still gets dumped into Puget Sound.

Bruce Nairn, an engineer in King County’s wastewater division, is working with state experts on the Salish Sea model to determine how much influence King County’s sewage effluent has on the health of Puget Sound. The model seems to show that nitrogen from King County’s treatment plants causes a significant problem in South Puget Sound. Yet Nairn contends that the effluent gets mixed with a far greater amount of nitrogen coming in with seawater from the Pacific Ocean. Furthermore, he said, much of that deep ocean water gets blocked and turned back by an underwater sill near the Tacoma Narrows Bridge.

“This is a state-of-the-art model,” Nairn said. “There are no fatal flaws in what they are doing. On the other hand, it is very complicated. In my experience, it is very difficult to calibrate this kind of model.”

Nairn and Ecology’s experts agreed to keep working together, along with others, to make sure the model reflects reality to the greatest extent possible.

Mindy Roberts, one of the original designers of the Salish Sea model, now directs the environmental group People for Puget Sound, a program within Washington Environmental Council.

“Every basin in Puget Sound acts differently,” Roberts said, “but what we have found is that the waters are far more connected than we thought. Local sources influence the local environment, but so do sources that are very far away.” 

The Salish Sea Model

Scientists say the Salish Sea Model will become one of the key tools for understanding the potential impacts of nutrients on Puget Sound.

The computer model is designed to account for practically every factor that comes together to create low-oxygen problems in one place but not another. Included in the calculations are the complexities of water circulation, the amounts and locations of nitrogen inputs, the growth and death of plankton, and the fate of organic and inorganic compounds in both the water and the sediments.

Because bacteria consume oxygen and expel carbon dioxide, the model also is designed to account for increased acidification resulting from low-oxygen conditions.

Findings so far suggest that sewage-treatment plants influence dissolved oxygen levels to a greater degree than upland sources of nitrogen that reach Puget Sound via river flows.

The Pacific Ocean plays a dominant role, as ocean currents bring nitrogen-rich water up from the depths and into Puget Sound through the Strait of Juan de Fuca. The amount of nitrogen from the ocean varies from year to year, often corresponding with short-term and long-term cycles such as El Niño and the Pacific Decadal Oscillation.

The effects of ocean nitrogen are greater in the Strait of Juan de Fuca and in the main body of Puget Sound than in the impaired inlets of South Puget Sound, which are farther away and more strongly influenced by local nitrogen sources, such as sewage-treatment plants, according to the model.

Without reductions in nitrogen, the model predicts increasing low-oxygen problems, especially in South Puget Sound, as the population increases and more nitrogen enters Puget Sound with increasing sewage effluent. Where and when to upgrade sewage-treatment plants with nitrogen-reducing equipment is becoming a major question. 

If nitrogen-removal systems were installed at the five largest plants, the population could double without increasing the amount of nitrogen going into Puget Sound, according to preliminary studies by Ecology. Installing the equipment at all treatment plants in Puget Sound could lead to a 40-percent reduction from current nitrogen loads.

Other solutions include reductions in agricultural runoff, which may include fertilizers and livestock wastes. Such actions have been credited with improving the health of Chesapeake Bay on the East Coast. Advanced septic systems are currently under study in Puget Sound and could help reduce nitrogen in areas that have poor soils or are close to shorelines.

In addition to reducing human nitrogen inputs, experiments are being conducted to see if natural systems can help, noted Ecology’s Bilhimer. In small bays that suffer from low-oxygen problems, mussel aquaculture may reduce the amount of plankton, while kelp and eelgrass beds could produce a bit more oxygen for the animals that live in those areas.

“We may need to do a little bit of everything,” Bilhimer said.


Salish Sea Model Domain (Version 2.0): expanded intermediate-scale grid extending out to the continental shelf.  Graphic: WA Ecology
The Salish Sea Model was developed by Pacific Northwest National Laboratory (PNNL) in collaboration with scientists at the WA Ecology Environmental Assessment Program. The model is a powerful computerized tool that has algorithms within it to simulate hydrodynamic and water quality processes. Graphic: WA Ecology


The Salish Sea model can be used to predict the effects that various actions can have on each and every location within Puget Sound. Accounting for population growth and land-use changes, the model is designed to answer questions such as: What would happen if half or even all the sewage-treatment plants installed nitrogen-removal equipment? What if farmers and other watershed sources reduced their nitrogen releases? And what is likely to occur as the climate continues to change?

It has taken years to design and test the model. Soon, according to Bilhimer, some answers should be available as a result of model runs scheduled for this year. After that, the team of experts with the Nutrient Source Reduction Project can focus on a cleanup plan — possibly, but not necessarily, a TMDL. At the same time, the team is developing an Implementation Strategy that will include a list of actions to be incorporated into the Puget Sound Action Agenda, the overall recovery plan for Puget Sound.

Working alongside the technical team, a large group of interested parties will help develop new policies and regulations, provide guidance to farmers and watershed residents and coordinate with ongoing ecosystem-recovery programs.

Chris Wilke, executive director of Puget Soundkeeper Alliance, says excess nitrogen is a growing problem in waterways across the country.

“We are not yet as bad as the Gulf of Mexico or Chesapeake Bay,” Wilke said. “I think there is still enough time and productivity in the Sound to begin reversing this and be able to say we dodged a bullet.”

Dead plankton leave clues to a food-web mystery

Algae bloom in Puget Sound near Edmonds, WA. Photo: Jeri Cusimano via WA Ecology (CC BY-NC 2.0) https://www.flickr.com/photos/ecologywa/8744775119High 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.

About the Author: 
Christopher Dunagan is a senior writer at the Puget Sound Institute.