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Spawning Habitat Integrated Rehabilitation Approach (SHIRA)

This research was specifically focused on rehabilitating salmonid spawning habitat in regulated rivers. This page contains some background information on spawning habitat restoration, a brief description of the SHIRA Approach and some links to relevant publications. The official SHIRA website is maintained by my collaborator, Professor Greg Pasternack

Photo of spawned out female chinook next to her redd at an spawning bed enhancement site on the Mokelumne River, California. ©2002 Wheaton (See Photo Copyright Disclaimer before downloading).


If you build it will they come? The very popular river restoration motive of rehabilitating spawning habitat for salmonids poses a range of interesting technical and scientific problems. Using the Lower Mokelumne River in California as a test bed, several experimental rehabilitation projects have been carried out and others are planned through 2009. This research was the focus of my Masters under the supervision of Dr. Greg Pasternack from U.C. Davis and in collaboration with Joseph Merz at East Bay Municipal Utility District (EBMUD). I am actively working on the extensive data sets we produced from the Mokelumne River.


The decline of salmonids in regulated rivers has been linked to many perturbations including over-harvest and the deterioration, inaccessibility and reduction of spawning habitat for these fish. Spawning habitat rehabilitation efforts have been underway since the late 1970s to attempt to replenish spawning gravels in gravel starved spawning reaches downstream of dams. In an inventory of gravel injection projects within California's Central Valley alone from 1976 to 1999, Lutrick and Kondolf (p. comm.) identified 73 spawning habitat rehabilitation projects, on 19 different rivers, totaling over US$ 45 million, and involving the addition of over 1.2 million cubic meters ( 1.8 million metric tons) of gravel. Spawning habitat rehabilitation can be segregated into three categories:

Contrast between regulated and unregulated river basins and context for spawning habitat rehabilitation activities. (Figure from Wheaton (2003) and Wheaton et al. (2004); ©2004 Wheaton; See Figure Copyright Disclaimer before downloading).

Types of Spawning Habitat Rehabilitation

1) Gravel Augmentation

Photo of Keswick Dam on Sacramento River by Kondolf ©1997 Elseiver Science (See Photo Copyright Disclaimer before downloading).
Gravel augmentation (also known as gravel injection or gravel replenishment) seeks to replenish some portion of a regulated river’s sediment budget deficit with imported sediment. This is typically achieved by dumping clean spawning gravels into piles along the edges of a river at locations upstream of degraded spawning habitat reaches (usually just downstream of a dam). It is assumed that augmented gravels will be entrained during high flows with the competence to transport them downstream. Designs are rarely necessary for gravel augmentation, but a sediment budget and a monitoring program to enable adaptive management are appropriate.

2) Hydraulic Structure Placement

The most common type of SHR is hydraulic structure placement (often called habitat enhancement or instream structures). Physical structures (e.g. large woody debris (LWD), boulder clusters, v-dams, half-log covers, deflectors) are placed in the channel to alter hydrodynamics in such a way that spawning gravels are deposited in the vicinity of the structures. The technique relies on an adequate supply of gravel from upstream and an active bedload transport regime to deliver it. Such structures may also be intended to provide refugia, cover and add habitat heterogeneity. In other instances, hydraulic structures are intended to promote pool scour. The implementation of hydraulic structure placement is typically prescriptive and usually lacks adequate process considerations.

Boulder Clusters on the lower Mokelumne River, CA.(©2004 Wheaton; See Photo Copyright Disclaimer before downloading).

3) Spawning Bed Enhancement

Construction on the lower Mokelumne River, CA.(©2004 Wheaton; See Photo Copyright Disclaimer before downloading).
Spawning bed enhancement includes direct modifications to the bed (e.g. riffle construction, bed ripping and riffle cleansing). Spawning bed enhancement that involves placement of gravel differs from gravel augmentation in that the augmented gravels are placed as specific bed features (typically riffles or bars), potentially providing immediate spawning habitat. Spawning bed enhancement can be used to improve the fluvial complexity of channels detrimentally simplified for flood control or mining purposes. Placed gravels are intended to decrease local depth and increase velocity to better match observed spawning preferences. Although bed enhancement may quickly provide usable spawning habitat, limited project lifespans may result without adequate consideration of geomorphic processes.

The SHIRA Approach

We developed SHIRA for use on salmonid spawning habitat rehabilitation projects in regulated rivers. The approach is driven by a mix of field data, conceptual models, and numerical algorithms to provide predictive and explanatory insight into the design and planning process. At the heart of SHIRA is a conceptual spawning model that explicitly identifies the assumptions behind the approach (see figure below). Although, this approach was developed specifically for spawning habitat restoration, many of its components are directly transferable to other forms of river restoration.
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Conceptual spawning habitat model. The arrows indicate influences, the circles represent processes and characteristics, and the boxes are the results. A combination of hydrogeomorphic processes spanning a range of scales combine to create physical habitat. Physical habitat is chosen by females for redd construction based on the ecologic functions provided by physical habitat and ecologic factors including habitat heterogeneity, run size, timing, social factors and physiology. The survival of alevins and ultimate emergence of fry is then primarily controlled by the substrate and local flow conditions during the incubation period. Figure 3 from Wheaton (2003): Conceptual Spawning Model.©2003

SHIRA flowchart. The two primary components are phases and modes. Projects progress sequentially through specific project phases, ranging from the initial problem identification to long-term monitoring and adaptive management. During each of seven phases, four primary modes are used to collect and analyze data on which informed decisions can be based. Figure 2 from Wheaton (2003) ©2003

Relevant References

The SHIRA website is the official repository for all SHIRA related publications and developments. In addition, the website includes examples of the application of SHIRA in different case studies on different rivers. Below, I only list the publications that I was directly involved with. For a detailed summary of the approach, check out the first paper below in the International Journal of River Basin Management. The second companion paper illustrates with a case study how design hypothesis testing under SHIRA is carried out. For further, less concise details, my Masters Thesis is provided. Please note that all PDFs are provided as courtesy copies only, and all copyrights are retained by the respective publishers).

Related documents from the Cosumnes-Mokelumne Paired Basin Project: Linked hydrogeomorphic ecosystem models to support adaptive management

Since Dr. Gregory. B Pasternack, Dr. Joe Merz and I first developed SHIRA, Eve Elkins and Rocko Brown have completed their masters at UC Davis extending and improving elements of SHIRA on the Mokelumne and Trinity Rivers. Additionally, Dr. Merz continues to implement and test SHIRA with EBUMD on the Mokelumne River. Check out Greg's research pages for more information.