Aquatic plants: unsung but prime salmon habitat

Photo by Carson Jeffres/UC Davis

A Chinook salmon in Big Springs Creek near Mount Shasta. Photo by Carson Jeffres/UC Davis, 2012

By Robert Lusardi and Ann Willis

For decades, California’s management and restoration of salmon and trout populations have focused on principles rooted in coastal redwood streams, mostly fed by rainfall runoff. These concepts portray ideal salmonid habitat as deep pools, shallow riffles and “large woody debris,” such as fallen trees and limbs.

Recent studies on spring-fed streams challenges this mindset. The findings strongly suggest these streams should play a larger role in the recovery and management of sensitive cold-water species, particularly salmonids.

Researchers at the UC Davis Center for Watershed Sciences found that trout in spring-fed streams grow faster than those reared in runoff streams in the same watershed.

Aquatic macrophytes in the spring-fed Shasta River. Photo by Robert Lusardi

Aquatic macrophytes in the spring-fed Shasta River. Photo by Robert Lusardi/UC Davis

Surprisingly, they suggest that trout benefit not only from the stable flow and temperature regimes of spring-fed streams but also from another dominant – yet much underappreciated – habitat feature: aquatic plants.

Known as macrophytes, these rooted vascular plants provide similar benefits as pools, and large woody debris.

As fish habitat, this woody debris provides structure, velocity heterogeneity and refuge from predators [1]. It also has been shown to increase habitat area and reduce competition between fish [2]. Similarly, biologists have long recognized pools as superior salmonid habitat for providing predator and thermal refuge, velocity heterogeneity and improved food resources [3].

Invertebrates in macrophyte habitat on Shasta River. Photo by Carson Jeffres/UC Davis

Hydopyschid caddisfly larvae spin nets to gather food in macrophyte habitat on the Shasta River. Photo by Carson Jeffres/UC Davis

Spring-fed streams generally lack the high volume flows of runoff streams that transport woody debris and scour pools. As a result, scientists and resource managers have paid less attention to the physical habitat dynamics of spring-fed systems than to other beneficial factors such as streamflow and water temperatures.

Macrophytes grow in many spring-fed streams and are largely a product of naturally occurring nutrients, stable flow and temperature, open canopy and low gradient. These plants provide many of the same benefits to trout and salmon of the more classic redwood streams type habitat.

Underwater tour of Big Springs Creek, by Carson Jeffres/UC Davis

On the Shasta River, a large spring-fed tributary to the Lower Klamath River, the UC Davis researchers conducted an experiment to understand the potential benefits of macrophyte habitat on juvenile steelhead trout.

Presented with multiple habitat types, steelhead overwhelmingly selected macrophyte habitat during spring and summer foraging. The researchers found that macrophyte habitat provided abundant food – the plants also are important for invertebrates – and refuge from high-velocity currents. This suggests that the use of macrophyte habitat allowed trout to gorge on seemingly unlimited food while exerting minimal energy.

Juvenile coho salmon in Big Springs Creek, by Carson Jeffres/UC Davis

Unlike more classic habitat forms, the effects of macrophytes on trout and salmon operate at larger spatial scales. Additional research on the Shasta River and elsewhere has shown that macrophytes increase stream water depth and wetted habitat area, and can reduce water temperature through shading [4]. Other studies have shown that macrophytes reduce competition between individual fish through visual isolation and increase fish density [5].

These broader benefits may be particularly important for salmonid populations in California during late summer and early fall, when flows in runoff streams typically decline and water temperatures rise.

Insect casings in Big Springs Creek, by Carson Jeffres/UC Davis

It’s no surprise that spring-fed streams such as Hot Creek in the eastern Sierra historically boasted some of the highest trout densities in California. Likewise, Shasta River historically supported 50 percent of the Klamath Basin’s Chinook salmon, even though it accounts for only 1 percent of the basin’s annual streamflow [6].

Pacific salmon recovery efforts in the Lower Klamath River drainage often focus on spring-fed systems such as the Shasta River because they provide flow stability and optimal thermal habitat for rearing salmonids.

While many factors contribute to fish production, macrophyte habitat has received far less attention for its beneficial effects on trout and salmon. Fully understanding such species-to-species interactions as those between plants and fish is important and will assist salmonid conservation planning and recovery.

Robert Lusardi is a post doctoral scholar in ecology at the UC Davis Center for Watershed Sciences and a California Trout-UC Davis Wild and Coldwater Fish Researcher. He studies stream ecology and food web dynamics of volcanic spring-fed ecosystems in Northern California. Ann Willis, an engineer who coordinates research programs at the Center, has done extensive fieldwork monitoring the restoration of Big Springs Creek.


[1] Crook, D.A. & Robertson, A.I. (1999) Relationships between riverine fish and woody debris: implications for lowland rivers. Marine and Freshwater Research, 50, 941-953.

[2] Sundbaum, K. and I. Naslund. 1998. Effects of woody debris on the growth and behaviour of brown trout in experimental stream channels. Canadian Journal of Zoology-Revue Canadienne De Zoologie 76:56-61.

[3] Nielsen, J.L., Lisle, T.E. & Ozaki, V. (1994) Thermally stratified pools and their use by steelhead in Northern California streams. Transactions of the American Fisheries Society, 123, 613-626; Rosenfeld, J.S. & Boss, S. (2001) Fitness consequences of habitat use for juvenile cutthroat trout: energetic costs and benefits in pools and riffles. Canadian Journal of Fisheries and Aquatic Sciences, 58, 585-593.

[4] Champion, P. D. and C. C. Tanner. 2000. Seasonality of macrophytes and interaction with flow in a New Zealand lowland stream. Hydrobiologia 441:1-12.

[5] Eklov, A.G. & Greenberg, L.A. (1998) Effects of artificial instream cover on the density of 0+ brown trout. Fisheries Management and Ecology, 5, 45-53.

[6] National Research Council (NRC). 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery; Wales, J. H. 1951. The decline of the Shasta River king salmon run. Bureau of Fish and Wildlife. California Division of Fish and Game

Further reading

Gregg WW, Rose FL. 1982. The effects of aquatic macrophytes on the stream micro-environment. Aquatic Botany 14: 309-324.

Beland KF, Trial JG, Kocik JF. 2004. Use of riffle and run habitats with aquatic vegetation by juvenile Atlantic salmon. North American Journal of Fisheries Management 24: 525-533.

Fausch, K. D. 1984. Profitable stream positions for salmonids – relating specific growth rate to net energy gain. Canadian Journal of Zoology-Revue Canadienne De Zoologie 62:441-451.

Jeffres, C., Aug. 24, 2011. Benefits of growing up in a spring-fed stream. California WaterBlog.

Lusardi, R. A. 2014. Volcanic Spring-fed rivers: ecosystem productivity and importance for Pacific salmonids. PhD dissertation. University of California, Davis.

Lusardi, R.A. 2013. How to save salmon: location, location, location. California WaterBlog

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7 Responses to Aquatic plants: unsung but prime salmon habitat

  1. nonewwater says:

    What a revelation, spring fed creeks are amazing salmonid habitat. Hot Creek environmental variables are super applicable to the rest of the State by the way, salmonids are totally native there especially the brown trout. The contention that managers have some how dropped the ball by focusing on non spring-fed ecosystem types is hilarious. How many spring-fed systems are actually below a natural barrier? How many man-made barriers are present on the ones without natural barriers? Ok, now how many streams do we have left? How much carrying capacity does this final list of streams have in terms of Chinook spawning area? Alright now that we have some reality applied to this article, how important are non spring fed ecosystems to Chinook managers in California? Maybe we should just plant Hydrilla throughout the Sacramento River, that would be awesome. Dear California Water Blog, please stop acting like Westlands when writing articles. Facts in their entirety please….

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