Significant river systems and environmental drivers for Chinook salmon stocks in Southeast Alaska 

Jessica Menges

The state of Alaska depends on successful fisheries to sustain its communities, provide jobs, and foster healthy ecosystems. The seafood industry directly employed 56,800 workers on average in 2015/2016. Nationally the Alaska seafood industry is worth $12.8 billion in economic output. Salmon are by far the most commercially valuable species in Alaska.

Pacific salmon, Oncorhynchus spp., are an ecologically and economically important species to the state of Alaska. In 2017 alone, the fishery was valued at $4.2 billion. Chinook salmon specifically support many different user groups in Southeast Alaska. These valuable industries include, a commercial fishery, personal/subsistence use, and a sport fishery.

Alaskans have been suffering from low runs of Chinook salmon since 2007. Specifically, in Southeast Alaska, Chinook runs hit an all-time low record in 2016. As a result it is crucial to understand what could be causing the collapse of these stocks and how these impacts can be mitigated or reversed. In order to manage the stock well it is imperative to know the location of important watersheds and rivers used for spawning, rearing habitat, adult habitat, and the environmental drivers that impact the overall abundance and health of the stock. Understanding these dynamics could allow policy makers and government organizations to protect certain streams, restrict fishing at certain times of the year where high abundance of juveniles are found, and organize awareness around anthropogenic impacts that change salmon abundances and the marine environment.

Chinook salmon lifecycle

In order to manage Chinook salmon effectively, it is important to understand their lifecycle. Chinook salmon are an anadromous species, meaning that they spend some of their life in freshwater and some in salt water. Chinook salmon travel from the ocean to freshwater rivers in order to spawn. Eggs laid on stream beds will eventually hatch into alevin, alevin develop into fry, fry to smolt, smolt to ocean stage, and ocean stage to spawning (figure 1). This cycle repeats perpetually and is referred to as “the great nutrient cycle.”8 Salmon bring nutrients from the ocean to freshwater streams. Anadromous fish such as salmon return to the streams in which they were born (natal streams) to spawn. Once in the streams they spawn and die. Their decaying bodies provide their young and the rest of the ecosystem with valuable nutrients. In order to find their natal streams Chinook salmon depend on olfactory senses, magnetic orientation, celestial orientation, and circadian calendar to find their natal steams. Chinook salmon’s olfactory senses are so precise that they can smell one drop of water from their natal stream mixed with 250 gallons of seawater.

Chinook salmon return to their natal streams to spawn after they have reached maturity, about 3-8 years. This mass migration and spawning event occurs between July and August. Every spawning Chinook salmon may lay between 1,000-17,000 eggs, but out of all these eggs approximately only 3 fish will return. For spawning, Chinook salmon prefer stream beds with large gravel, a strong current, and that are in deep water.

Understanding Chinook salmon’s preferred spawning habitat, life cyclevulnerabilities, and detrimental impacts to their olfactory senses are vital to effectively managing this ecologically, culturally, and economically important species.

Chinook Salmon Stocks of Concern

According to the Alaska Department of Fish and Game, “The Policy for the Management of Sustainable Salmon Fisheries (SSFP; 5 AAC 39.222, effective 2000, amended 2001) directs the Alaska Department of Fish and Game (ADF&G) to provide the Alaska Board of Fisheries (Board) with reports on the status of salmon stocks and identify any salmon stock that present a concern.” ADF&G groups stocks into three different groups: yield concern, management concern, and conservation concern.15 According to ADF&G “A stock of Management Concern is defined as “a concern arising from a chronic inability, despite the use of specific management measures, to maintain escapements for a salmon stock within the bounds of the Sustainable Escapement Goal, Biological Escapement Goal, Optimal Escapement Goal, or other specified management objectives for the fishery.” Three out of the five Chinook salmon stocks in southeast Alaska are registered as stocks of concern. More specifically, the Chilkat River system, the King Salmon River system, and the Unuk River system are all classified as management concerns.

On the accompanying map all of the Chinook salmon river systems in southeast are shown. These include the Chilkat River system, the Taku River system, the Sitikine River system, the King Salmon River system, and the Unuk River system. Within these mapped water systems, areas of Chinook salmon spawning are marked with red circles, rearing with green circles, and present (adult stage) with purple circles. Each circle is placed either at the beginning or end of a waterway to designate that whole branch of the river as spawning, rearing, or present.

Water Temperature

Temperature changes impact Chinook salmon throughout all of their different life stages. In the spring alevin-stage Chinook salmon emerge from the gravel and still have a yolk sac attached to their ventral or belly side. Larval fish rely on the yolk absorption for growth and development before they can feed. The larger larvae are stronger, better swimmers, and less susceptible to predation. Heming (1982) found that the rate of yolk sac absorption in alevin salmon larvae varied directly with temperature. Specifically, as temperature increased, the rate of yolk sac absorption increased. This is because of the increased “maintenance” costs and metabolic demand at higher temperatures. Increasing the rate of yolk absorption to address increased metabolic costs decreases the amount of energy left for tissue growth and actually leads to an energy deficit. Metabolic energy deficits experienced in the yolk phase leads to a reabsorption of developed tissue. As a result, high rearing temperatures (great than 10°C) led to reduced survival, hatching very early, and smaller fish when hatched. In conclusion, increased stream temperatures result in smaller, weaker, more vulnerable Chinook alevin larvae.

Increased water temperatures can also adversely impact smolt-stage Chinook salmon. Survival after smolting is maximized if the timing aligns with migration from fresh to marine waters. Smolting is “an adaptive specialization for downstream migration, seawater entry, and marine residence. While still in fresh water, smolts become silvery and streamlined...and begin schooling.” Sykes, et al. (2009) found that warmer water temperatures resulted in early migration before smolting occurred. This could cause increased vulnerability and decreased survival in Chinook salmon smolt.

Finally, increased water temperatures can negatively impact adult, migrating Chinook salmon. Goniea, et al. (2005) found that increased water temperatures led to a change in migration behavior. Specifically, migration rates slowed with increasing temperature because salmon were actively seeking out cooler tributaries to take refuge from warmer river areas. Changing migration rates could have a ripple effect on the timing of the rest of the salmon life cycle. Additionally, Chinook salmon stop feeding once they begin their migration to their spawning grounds, burning extra energy escaping warm water temperatures could have detrimental impacts on the spawning process.

The accompanying map displays Chinook salmon streams (spawning, rearing, present) in relation to average sea surface temperature.

Pacific Decadal Oscillation

Pacific Decadal Oscillation (PDO) is a climactic phenomenon similar to El Nino, but
may persist for decades. PDO is caused by winter wind directions in the North Pacific and can cause both “warm” and “cold” cycles. The cycles are well correlated with changes in climate, ecology, sea level pressure, terrestrial and ocean temperatures, precipitation, stream flow, and commercial fish landings. Evidence supports the hypothesis that Chinook salmon are sensitive to changes in ocean temperatures and PDO fluctuations. Mantua, et al. (1997) were the first to find a correlation between PDO and salmon returns. PDO impacts air temperatures, biological productivity, and stream flow. Below average runs of Chinook salmon align with warm PDO cycles. This is logical because of what is known concerning Chinook salmon and increases in water temperature.

Using this data and what we understand about increased water temperatures and PDO cycles, predictions may be made concerning year class strength in relation to projected changing ocean temperatures.

Chlorophyll a & Plankton Abundance

The accompanying map shows the average chlorophyll a levels (mg/m3) in June 2017, in Southeast Alaska. Chlorophyll a is a pigment that phytoplankton utilize during photosynthesis. Photosynthesis is the chemical process phytoplankton undergo that produces energy; this energy fuels the rest of the food web when they are consumed. As a result, measuring chlorophyll a can serve as a proxy measurement for primary phytoplankton production. Phytoplankton are the basis of the marine food web and serve as the primary source of energy for many organisms including zooplankton.

Increased chlorophyll levels indicate increased abundances of zooplankton, whichmeans more food for yearling salmon. This is because yearling Chinook salmon’s diet consists largely of zooplankton. Peterson, et al. (2010) found that chlorophyll levels positively correlated with Chinook salmon yearling abundances. In other words, as chlorophyll levels and presumably phytoplankton levels, increased so did Chinook salmon yearling abundances. Peterson, et al. (2010) also found that high and healthy levels of chlorophyll a indicates good juvenile salmonoid habitat.

However, there can be too much of a good thing when it comes to chlorophyll a levels. Large influxes of nutrients into the marine environment can cause phytoplankton blooms. These phytoplankton blooms or mass multiplication of photosynthetic algae, deplete the localized water of oxygen, which can result in large kills of marine organisms. As a result, it is important to monitor sources of ocean fertilization and run off such as agricultural sites to limit the likelihood of a bloom.

Snow Water Equivalent

Snow water equivalent is a snowpack measurement, essentially it is a calculated value that represents the depth of water that would result when the snow melts.

Warming climatic temperatures lead to earlier snowmelt and a lower proportion of precipitation falling as snow compared to rain. In the winter, increased precipitation as rain rather than snow leads to elevated stream levels that scour the stream bed and destroy salmon eggs. In the summer and fall, less snowpack leads to a reduction in spawning habitat and further increases stream temperatures. In other words less snowpack means less run off into the streams leaving sections or entire streams dry, which removes large areas of spawning habitat. Additionally, higher volumes of water flowing through the streams cools the water via advection and much greater amounts of solar energy are required to heat larger volumes of water. Snowmelt also provides an influx of water that cools the streams.

The accompanying map shows a projected decrease in snow water equivalent from historical to 2020 (% change from historical), to 2050 (% change from historical), and to 2080 (% change from historical). Decreased snowpack is a direct result of increased atmospheric temperature and climate change. It is extremely important to understand anthropogenic changes impact salmon streams to effectively advocate for change.

Ocean Acidification and pH

Burning fossil fuels emits excessive amounts of CO2 into the atmosphere. This CO2 is then absorbed by the ocean, which induces a chain of chemical reactions. These chemical reactions result in an abundance of hydrogen ions (H+), which increase the acidity of the ocean. Not only does CO2 decrease the pH, but it binds readily with carbonate ions and water. Carbonate ions are utilized by shelled organisms in the process of calcification (building shells and cuticles, figure 4). The lack of free carbonate ions can stunt growth rates or even cause reabsorption of carbonate from shelled organisms resulting in pitting and fragility.

One of the many groups of organisms that are being impacted by ocean acidification are mollusks. Mollusk is a large phylum that contains invertebrates, most of which have an external calcareous shell. Ocean acidification dissolves the shells of mollusks, which are an important food source for Chinook salmon.

Salmon rely upon olfactory senses to detect and avoid predators. Increased pH is known to negatively impact or render these senses useless. Leduc, et al. (2011) found that salmon in acidic streams didn't respond to alarm chemical cues, while salmon in neutral streams exhibited typical alarm responses.44 This means that salmons’ ability to avoid predators and detect prey is negatively impacted by ocean acidification. Salmon use the same olfactory sensory system to detect alarm cues as they do to return to their natal streams. This means that in acidic water salmon may be unable to successfully navigate to their natal streams.

Modeling and monitoring ocean acidification scenarios is extremely important for ensuring the stability of the Chinook salmon stock. If the rate of ocean acidification does not decrease, we may see a ripple effect throughout the entire marine ecosystem that eventually impacts higher tropic level species such as Chinook salmon.


This map can be used to inform resource management and policies concerning land management, coastal development, fisheries management, environmental preservation, etc. Policy makers need to understand how environmental protections also benefit the health of fishery stocks, and every individual needs to understand how their consumer choices impact the health of the environment.

Salmon are a part of a wider ecological system in the Gulf of Alaska and eastern Pacific. Being informed on all of the ecological, climactic, physiological, trophic, and physical links between Chinook salmon and other systems only fosters better-informed management practices. I believe that this map has accomplished the goal of providing a holistic, encompassing, and accessible view of Chinook salmon in Southeast Alaska.


This project was made possible with data from and the help of Aurora Lang, Alaska Sustainable Fisheries Trust, Alaska Longline Fishermen’s Association, Linda Behnken, Dan Falvey, Steve Lewis, Katy Echave, National Oceanic and Atmospheric Administration, Stacey Buckelew, Alaska Ocean Observing System, National Aeronautics and Space Administration, and Alaska Department of Fish and Game.

Map Data Sources:

Anadromous fish catalog (spawning, rearing, present) data, 2014 (ADFG); Chinook stocks of interest data, 2015 (ADFG); bathymetric data (AOOS & NOAA); temperature (AOOS); snow water equivalent data, 2018 (USFS); and chlorophyll a (NASA).