Fish Habitat in Downtown Seattle

Threats to an important ecosystem

Photo: Tavish Campbell

Shallow ecosystems facilitate the development and survival of juvenile fish. Estuaries in particular are productive and provide fish with high abundances of small invertebrates from terrestrial, aquatic, and benthic habitats. In addition, predators are rare or ineffective in the confined spaces of shallow waters. Thus, shallow areas are often fish nurseries.

Seawall along Harbor Avenue at Duwamish Head, West Seattle
Photo: Hugh Shipman


While shorelines are important to fish, they are also important to people. For millennia people have benefited from living close to the water and have engineered waterfronts. Two of the more common modifications to shorelines are armoring (e.g., seawalls, riprap, bulkheads) and overwater structures (e.g., piers, floating docks). Despite widespread use of shoreline modifications, we have only recently studied their ecological effects. This is concerning because shoreline modifications dramatically change the shallow environments that fish depend on.

Pacific salmon

Photo: Tavish Campbell

Among the fish likely to be affected by shoreline modifications are Pacific salmon. These fish hatch in rivers and migrate through estuaries on their way to oceans (some also reside in estuaries long-term). Estuaries are important to juvenile salmon because they provide prey, protection from predators, and transition zones that allow fish to adapt to increasing salinities. Feeding is critical for juvenile salmon because they need to outgrow potential predators, fuel migration, and store energy to survive their first winter. During their estuarine migrations, salmon often swim within a few meters of shore, and co-occur with any modifications to shorelines.

Salmon are culturally, ecologically, and economically important. Salmon are an iconic species in the Pacific Northwest and have been sustainably harvested for thousands of years. Native Americans have long celebrated salmon returns, and no TV broadcast of Seattle is complete without a shot of people throwing salmon around Pike Place Market. Salmon are also keystone species. When adults return to their natal rivers to spawn and die, they deliver limiting nutrients to hundreds of other species, including bears, eagles, and trees. Salmon are also worth a lot of money. They support billion dollar fisheries and their associated jobs, local and tourist fishers, and food industries. Despite their value, habitat degradation has been implicated in the decline of many salmon populations, resulting in their listings under the Endangered Species Act (ESA).

Elliott Bay seawall reconstruction

Photo: Seattle Municipal Archives

The original seawall along downtown Seattle in Elliott Bay was built in the 1930s. The 2001 Nisqually Earthquake, along with long-term damage from wood-boring gribbles, put the seawall into a state of disrepair. The city needed to replace the seawall and elected to design a waterfront that would provide better habitat for fish, especially juvenile salmon. Salmon in this system, including Chinook salmon listed as threatened under the ESA, migrate through estuarine waters of Elliott Bay from the Duwamish River.

A major component of my group’s research was to document what was “wrong” with current habitat along the downtown waterfront so that future efforts could target compromised habitat functions. In particular, we were concerned with ecological effects of seawall armoring and large overwater structures.

Effects of pier shading on fish distribution and behavior

Photo: Andrew Buchanan


Much of the waterfront along downtown Seattle is shaded by piers. These piers are relatively large and the areas under them are quite dark. Many fish, including juvenile salmon, rely on visual cues for essential activities such as feeding, schooling, and avoiding predators. Previous reports suggested that salmon are reluctant to swim into shaded areas created by large piers, probably because their eyes adjust slowly to changes in lighting. These reports observed salmon swimming in circles next to piers for several hours, generating concern that piers may delay salmon migrations.

My group designed a study to survey fish near three piers along the downtown Seattle waterfront. We surveyed fish visually by snorkeling at the surface. When we saw fish, we noted their species, school size, presence/absence of feeding behavior, and their location relative to the piers.

Fish were uncommon under piers, and salmon were often observed next to the shade cast by piers. When salmon did occur underneath piers, they fed less often than in sunlit areas. In general, most species appeared to avoid shaded areas, except for red rock crabs that were often observed in the shade. Thus, areas under piers appeared to provide poor fish habitat, and our study supported concerns that piers along Seattle’s waterfront may delay salmon migrations.

Effects of Piers on Fish.png
We rarely observed fish underneath piers, and salmon aggregated next to shading.
Salmon Migration Piers.png
Salmon swim along the shoreline, and those migrating through downtown Seattle encounter many piers that may disrupt their migrations.

Given that removing piers along the waterfront is impractical, one option to improve fish habitat is to reduce their shading. The year following our snorkel surveys, engineers installed three light penetrating surfaces into Pier 62/63. These surfaces allowed more light to reach the water, and we observed a more even distribution of fish relative to the pier. While these results are preliminary (only one pier was treated & we observed a different fish assemblage between years), it suggests that some negative effects of piers can be mitigated by integrating translucent materials into their surfaces. The city decided to create a salmon migration corridor using light penetrating surfaces that spans the entire length of the waterfront, which will be interesting to evaluate in the future.

LPS Aquarium.png
Light penetrating surfaces were installed into Pier 62/63 to allow more light to reach the water.
In a pilot study, light penetrating surfaces (LPS) were installed into a pier to allow more light to reach the water. After the LPS were installed, we observed a more even distribution of salmon relative to the pier.


Relevant publications: 

Munsch SH, Cordell JR, Toft JD, Morgan EE. 2014. Effects of seawalls & piers on fish assemblages & juvenile salmon feeding behavior. North American Journal of Fisheries Management 34: 814-827.

Cordell JR, Toft JD, Munsch SH, Goff M. 2017. Benches, beaches, & bumps: how habitat monitoring & experimental science can inform urban seawall design. In eds. Bilkovic DM, Mitchell MR, Toft JD, La Peyre MK, Living Shorelines: The Science & Management of Nature-based Coastal Protection


Effects of seawalls on fish assemblages

We compared fish assemblages along beaches and seawall shorelines. Studies in other locations had shown that shoreline armoring affected the local assemblage composition of fish, but none of them had examined fish behavior directly. That is, they used nets or sonar to sample fish, which precluded behavioral information, and  it was unclear whether assemblage differences were caused by fish selecting for certain types of substrate.

In this study, we used scuba to survey fish at three beaches and along three seawall sites in Elliott Bay. Beaches were artificially constructed along waterfront parks. Seawall sites were located along the seawall where the seawall and riprap had truncated the intertidal area. In addition to recording basic survey information, we noted which substrate type the fish were closest to. We found that fish assemblages were significantly different between these site types, and that the fish that were most affected were those that selected for a certain substrate type (e.g., boulders, sand). These fish often had obvious connections to certain substrates, such as flatfish and crabs that burrowed in sand to avoid predators. Thus, it appeared that shoreline engineering could affect habitat value.

This study also raised important questions on how to manage habitat that was substantially removed from its historical condition. Elliott Bay, for example, was historically comprised of beaches and mudflats similar to the artificial beaches we surveyed. Should we attempt to manage for the historical fish assemblage in Elliott Bay, or the one that is currently present? Do our views change if we consider that restoring Elliott Bay to historical conditions is quite unlikely? A new beach is being installed as part of the waterfront reconstruction, and it will be interesting to see if the fish assemblage changes to reflect the habitat types that the beach provides.


We observed different fish & crabs along beaches and armored shorelines. Differences in fish abundances were most apparent in species that selected for a specific substrate type.

Relevant publication:

Munsch SH, Cordell JR, Toft JD. 2015. Effects of shoreline engineering on shallow subtidal fish & crab communities in an urban estuary: a comparison of armored shorelines & nourished beaches. Ecological Engineering 81: 312-320.


Effects of seawalls on juvenile salmon diets

Under natural conditions, shallow waters produce prey in the substrate that are major prey items for juvenile salmon. However, armoring eliminates heterogeneous substrate in shallow areas, which may reduce prey availability.

We sampled (1) prey from the water column and (2) diets from juvenile salmon along beach and armored shorelines. We found that epibenthic copepods, a major prey item for juvenile chum salmon, were less abundant along armored shorelines. We also found that chum salmon fed almost exclusively on epibenthic copepods when they were available, and switched to feeding on plankton along armored sites. This was concerning because epibenthic copepods are brightly colored and thought to be poor swimmers, thus salmon may waste energy along armored shorelines feeding on prey that are harder to see or capture.

Juvenile chum salmon along beach shorelines consumed mostly epibenthic copepods while those along armored shorelines consumed mostly planktonic copepods. Epibenthic copepods were more abundant along beach shorelines.

A new beach, textured seawalls, and artificial intertidal zones (i.e., habitat benches) are being implemented along the reconstructed waterfront. These habitat features are anticipated to provide greater prey availability than the previous featureless seawall shorelines.

Relevant publications:

Munsch SH, Cordell JR, Toft JD. 2015. Effects of seawall armoring on juvenile Pacific salmon diets in an urban estuarine embayment. Marine Ecology Progress Series 535: 213-229

Cordell JR, Toft JD, Munsch SH, Goff M. In Press. Benches, beaches, & bumps: how habitat monitoring & experimental science can inform urban seawall design. In eds. Bilkovic DM, Mitchell MR, Toft JD, La Peyre MK, Living Shorelines: The Science & Management of Nature-based Coastal Protection

Toft JD, Ogston AS, Heerhartz SM, Cordell JR, Flemer EE. 2013. Ecological response and physical stability of habitat enhancements along an urban armored shoreline. Ecological Engineering 57: 97-108.

Effects of seawalls on ontogenetic habitat shifts of juvenile salmon

Animals must often balance needs to avoid predation with other habitat benefits (e.g., feeding). For example, areas that have the most food are often the most exposed to predators. Fish in shallow waters may experience this tradeoff when they decide how deep of water they should occupy. Shallow areas are probably relatively safe (because predators are less common or ineffective), but fish that confine themselves to shallow areas may miss out on habitat benefits such as expansive foraging spaces in open waters, or they may become ineffective swimmers if the water is too shallow.

In this study, we used snorkel surveys to compare (1) the size of juvenile salmon with the depths that they occupied and (2) the size distribution of fish in the shallowest available waters along low-gradient shorelines (e.g., beaches & an intertidal habitat bench) with those where shoreline armoring had eliminated shallow areas.

We found that juvenile salmon shifted to deeper waters as they grew. However, this trend was not present along armored shorelines, potentially meaning that smaller fish are forced to occupy inappropriately deep (dangerous) waters when armoring eliminates shallow areas.

Many fish use shallows and shift to deeper waters as they grow, but our study was the first to show that this shift occurs on a fine enough scale that destruction of the intertidal zone (by armoring) can interfere with habitat shifts. This is especially concerning because shallow areas are disappearing worldwide as sea levels rise against built shoreline (i.e., coastal squeeze).

Shallow waters created by the new beach and intertidal habitat benches along the downtown Seattle waterfront will hopefully allow fish to occupy appropriate depths for their sizes.

Juvenile salmon shifted from shallow to deeper waters as they grew. We did not observe this transition at armored sites where there were no shallow waters.
Habitat Shifts Squeeze.png
As sea levels rise against built shorelines, smaller fish may be forced to occupy inappropriately deep waters.

Relevant publication:

Munsch SH, Cordell JR, Toft JD. In Press. Fine-scale habitat use & behavior of a nearshore fish community: habitat partitioning, nursery functions, & avoiding predation. Marine Ecology Progress Series doi: 10.3354/meps11862. Feature Article


We found that shoreline armoring and overwater structures compromised habitat functions and processes including habitat connectivity, provision of prey, and ontogenetic habitat shifts. Many of these lost functions can be at least partially restored within the constraints of urban shorelines through innovative solutions such as light penetrating surfaces in piers, artificial intertidal zones in front of seawalls, artificial beaches, and textured seawall faces. Beaches in particular are promising solutions to urban waterfronts: they provide recreational spaces for people that allow them to connect with nature (not always an easy task in an urban landscape) and they also provide fish with better habitats than featureless shorelines. Ideally, shorelines will be designed so that “everybody wins;” that is, fish and people benefit.

Publication that reviews everything we know about effects of armoring and overwater structures on fish:

Munsch, S. H., Cordell, J. R., & Toft, J. D. (2017). Effects of shoreline armouring and overwater structures on coastal and estuarine fish: opportunities for habitat improvement. Journal of Applied Ecology.