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Cramer Fish Sciences: Lancaster Road Side Channel and Floodplain Restoration   Innovative Scientific Solutions for Fisheries and Environmental Challenges  
Cramer Fish Sciences
"In collaboration with Dr. Paul Anders at Cramer Fish Sciences, we were able to develop a truly innovative approach to subbasin planning in the Kootenai. Aspects of our plan became a model for other subbasin plans across the Columbia River Basin. Paul's contribution, along with his professionalism and hard work, was a big reason for that."
David Rockwell
Natural Resource Consultant

PROJECT: Lancaster Road Restoration




In 2008, Cramer Fish Sciences (CFS) was awarded a grant from the U.S. Fish and Wildlife Service (USFWS) Anadromous Fish Restoration Program (AFRP) (Grant #813328G012), for the Lancaster Road Side Channel and Floodplain Restoration Project (Project). Key goals of the Project were to rehabilitate and enhance productive juvenile salmonid rearing habitat in the Stanislaus River; and determine project effectiveness with an efficient and scientifically robust monitoring program. In order to adaptively implement restoration from its inception to its completion, the project was conducted in three phases: Phase I - Design, Outreach and Permitting; Phase II - Implementation; and Phase III - Post-implementation monitoring and continued outreach. The CFS team worked closely with the local community and resource agencies throughout each phase of the project.

L-R: View of the Lancaster Road side channel shown before construction (July 20, 2010), after construction (January 1, 2011), and inundated at ~3000 cfs after construction (April 18, 2012).

[Click each picture to view in high resolution]

Phase I of the project began during fall 2008 and included plan development for project design, monitoring, community outreach, pre-project monitoring, and fulfilling construction regulatory requirements. The CFS team worked with engineers and local landowners to define project goals and design standards, develop specific monitoring objectives to measure project success, and finalize a project design plan. Phase II included site construction, regulatory monitoring, and ongoing public outreach activities. Phase III began immediately after construction and included post-construction implementation, effectiveness, and validation monitoring; fulfilling post-construction permitting requirements; and ongoing public outreach activities.

Final construction included development of a side channel and three tertiary channels. Following construction, total Chinook Salmon fry habitat increased about threefold depending on flow, although this decreased slightly after two years of monitoring. Total juvenile Chinook Salmon habitat nearly doubled in the project site; relative increase in habitat was dependent on flow. This resulted in increasing average Chinook Salmon abundance in the restored areas by 2013. Juvenile steelhead habitat increased slightly post-construction, and increased more substantially two years after project completion.


The Project vision is to restore critical habitats for juvenile salmonids and, in coordination with local communities and stakeholders, promote recovery of healthy and diverse Chinook salmon and steelhead populations in the Stanislaus River, while helping meet the AFRP abundance goals. This vision fits into the framework of salmonid population recovery on the Lower Stanislaus River and is aligned with the following AFRP goals to: 1) involve local partners in the implementation and evaluation of restoration actions; 2) improve habitat for all anadromous life stages through improved physical habitat; and, 3) collect fish population, health, and habitat data to facilitate evaluation of restoration actions (USFWS 2001). The vision also meets objectives outlined in previous planning efforts for the Stanislaus River (CFS 2009) by working to improve our understanding of Stanislaus River salmonid population dynamics.

The Stanislaus River Restoration Plan was used to help identify critical limiting factors and knowledge gaps in order to assess and prioritize research and habitat restoration actions for these valuable resources. The Restoration Plan also provided a basis to recommend both adaptive restoration and applied research specific to this project to more effectively address AFRP goals. Within this context we developed the following goals for the Project:

  1. To serve as an example of publicly-supported applied fisheries and restoration science;
  2. To rehabilitate and enhance productive juvenile salmonid rearing habitat in the LSR; and,
  3. To determine project effectiveness with an efficient and scientifically-robust monitoring program.

These project-specific goals fit into the framework of AFRP, and meet the AFRP and CALFED requirement to use adaptive management in planning, design, and implementation (CALFED 2001).

Regional location of the Lancaster Road Side Channel Restoration Project, Stanislaus River, CA. Inset maps show the project site in relation to the state of California and surrounding cities. Below is an aerial view of the project area, showing the geographical extent of the project site and the side channel and tertiary channels (TC1-TC3) that were constructed. The Stanislaus River flows from right to left.


Flow measurements

CFS employee taking flow measurements to understand how restoration actions affected river depth and velocity.

CFS employs three types of monitoring to investigate the impacts of restoration projects: implementation monitoring; effectiveness monitoring; and validation monitoring. The goal of implementation monitoring is to determine whether the restoration project was executed according to the design plan and whether it met the original goals, specifically with respect to physical structure and hydrology. The main goal of effectiveness monitoring is to determine whether the project met restoration objectives. Site-specific effectiveness monitoring tracks physical conditions and biological responses necessary to provide productive rearing for juvenile salmonids. Validation monitoring is carried out to determine if the basic assumptions behind the project conceptual model are valid. For this project, validation monitoring consisted primarily of evaluating whether side channel construction restored floodplain processes.

Monitoring projects sought to answer such questions as:

  1. Do constructed topography/bathymetry and duration and magnitude of flooding match design plans?
  2. Following restoration, does the channel inundate at flow levels present during the juvenile rearing period?
  3. Was there an increase in inundation duration and habitat availability?
  4. Was the side channel utilized by juvenile Chinook Salmon and steelhead, and were juveniles associated with specific habitat characteristics (depth, velocity, vegetative cover)?



To determine if the construction met project goals, CFS compared the "as-built" elevations to the specified elevations. The following figure shows that of the entire side channel footprint, ~70% of survey points were on grade (0.01 in. accuracy). Of the remaining area, 46% was on average 0.19 in. too high, and 54% was 0.20 in. too low. These data suggest the site was constructed appropriately to design specifications.

Comparison of channel bathymetry for site designs and post construction at the Lancaster Road Restoration Project, Stanislaus River, CA. Yellow indicates little to no change, blue indicates lower areas than specified, and red indicates higher areas than specified.

Bathymetric comparison of pre- (A), immediately post (B), and ~22 months post-channel construction (C). This figure highlights the connection of the side channel to the main reach of the river, and shows how flow changed, including in the tertiary channels, after construction.

Habitat area

For Chinook Salmon juveniles, Weighted Usable Area (WUA) nearly doubled immediately following construction under 900 ft3/s flows, from 530.4 m2 WUA (7.4% of total wetted area) to 1001.3 m2 WUA (12.1% of total wetted area). There was also a substantial increase in WUA under the higher flow conditions, with an additional 545 m2 WUA under 1200 ft3/s and 493.5 m2 under 1500 ft3/s, and corresponding increases in the percent of wetted area with suitable juvenile Chinook Salmon habitat. Following two seasons of periodic inundation, WUA remained relatively constant, with habitat increasing by 12.2-44.2 m2 (0.1%-0.5% wetted area) depending on flow.

River 2D modeling visual representation of modeling results for Chinook Salmon juvenile habitat before restoration (PRE), immediately after restoration (POST 1), and two years following restoration (POST 2), under three simulated flow conditions (900 ft3/s, 1200 ft3/s, and 1500 ft3/s). Warm colors indicate higher quality habitat and cool colors indicate lower quality habitat.

Snorkel surveys

CFS employee performing snorkel surveys to monitor use of the restored area by salmonids and other fish species.

Habitat use and abundance

Following restoration, the side channel inundated each year (2012 and 2013) for 30-60 consecutive days. During this time, juvenile Chinook Salmon and steelhead utilized the side channel and tertiary channels extensively. There were high Chinook Salmon abundances in both 2012 and 2013. In 2012, steelhead were also abundant. Very few steelhead were observed in 2013; this may have been due to an extremely high flow event (flows > 3000 ft3/s) that occurred in late April/early May, during the time of year when juvenile steelhead are typically observed in the system. It is likely that juvenile salmonids in both the main channel and the side channel were actively transported out of the system by high stream velocities.

We generally did not observe significant abundance differences between the side channel and margin (edge) habitat of the main channel following restoration. The River 2D model predicted that some suitable salmonid rearing habitat would occur along the main channel bank margins, and these were also the areas where the snorkel surveys could be safely conducted. In 2012, Chinook and steelhead abundances in the side and tertiary channels were comparable with those observed in margin habitats of the main channel control sites. In 2013, Chinook abundances were similar between the main channel and side channel, but lower in two of the tertiary channels. The lower number of fish observed in the tertiary channels were likely due to low flow conditions and lack of instream vegetative cover in the tertiary channels. The two-dimensional model predicted that little suitable habitat would be available in the tertiary channels under the lowest modeled flow conditions, and surveys conducted under these conditions likely contributed to the lower average abundance in the tertiary channels. In addition, there was less vegetative cover available in the tertiary channels as compared to the side channel, and we observed a significant association with instream vegetative cover for both Chinook Salmon and steelhead juveniles. It is important to note that the tertiary channels were constructed to provide habitat at higher flows than those optimized in the secondary channel and this appears successful.


As has been found in previous studies, strong associations were observed between fish abundance and vegetative cover features (large and small woody material, submerged trees, low-velocity edge habitat) (Fausch 1993, Moyle 2002, Gard 2006, Beakes et al. 2012). These features provide increased structural complexity, creating a refuge from high streamflow and predators in the main channel and promoting fish production and survivorship (Willis et al. 2005; Schneider and Winemiller 2008). Studies on the Lower American River suggest that, in addition to being associated with higher fish abundance, instream cover features may also increase juvenile salmonid foraging behavior, provided that the cover feature provides a velocity break (CFS 2013). These velocity breaks presumably allowed fish to allocate more energy towards feeding and less towards maintaining position in the water column. The potential bioenergetic benefits of inchannel structure to rearing salmonids have been described in several studies and have been effectively used to predict microhabitat selection and fish density (Lehane et al. 2002, Hayes et al. 2007, Jenkins and Keeley 2010, Urabe et al. 2010 Gustafsson et al. 2012). On the Stanislaus River, predation from non-native fish species has also been identified as a potentially significant cause of juvenile salmonid mortality, and cover features may also provide a refuge from top predators such as bass.

Drift nets

CFS employee performing drift net surveys to monitor drift macroinvertebrates in one of the tertiary channels, post-construction.

Food availability

Food availability, particularly drift macroinvertebrates, is a critical but often discounted component of juvenile salmon habitat restoration projects. The restored side channel and tertiary channels in this study resulted in an overall increase in the total amount of aquatic and riparian habitat and, as a result, undoubtedly increased the total amount of both aquatic and terrestrial invertebrate drift available as prey to juvenile salmonids. The amount and type of drift at the study site varied by year and date and was likely affected by the amount of time the stream channel was inundated, weather conditions, time of day, and canopy. There is a real management need to develop methods and measures for monitoring and assessing the quality and quantity of the food supply, particularly drift, to support juvenile salmonid growth in restoration projects. This study was an important first step.


The Lancaster Road side and tertiary channels provided suitable habitat characteristics (depth, velocity, and vegetative cover) for juvenile Chinook Salmon and steelhead. The total area and relative proportion of usable habitat was higher following construction under a range of flow conditions. Observations of habitat associations in the side channel suggest that side channel habitats may offer an important refuge from the prevailing high-velocity conditions in the main channel, and that the availability of instream vegetative cover may be at least as important as depth and velocity metrics typically used to calculate habitat suitability.

Core sampling

CFS employee core sampling to understand how placed gravel, cobble, and fines move over time due to river flow.

We did not evaluate residence time of juvenile salmonids in side channel habitat, as compared to the habitat in the bank margins of the main channel. Future studies could examine whether the improved side channel habitat conditions lead to higher retention and growth of juvenile salmonids prior to outmigration. Other studies have shown that juvenile salmonids that spend more time rearing instream before emigrating enter the ocean at a larger body size and have greater survivorship (Unwin 1997; Sommer et al. 2001; Woodson et al., in press). Thus, enhancing low-velocity juvenile rearing habitats such as side channels and floodplains has the potential to improve retention of juveniles in the river system, increasing the quantity and quality of juveniles entering the ocean and likelihood of survival. This hypothesis could be tested by tracking fish microhabitat utilization, retention, and growth in both the main and side channels using mark/recapture and tracking techniques.

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