Monterey Peninsula Water Management District


DRAFT Technical Memorandum 2008-01


Alternative Adult Steelhead Counting Technology to Enumerate Upstream Migrants and Estimate the Total Run Size of South Central Coast Steelhead in the Carmel River Watershed After Removal of San Clemente Dam


June 16, 2008


Prepared by

Kevan Urquhart




California American Water (CAW) has been required by the California Department of Water Resources (DWR) Division of Safety of Dams (DSOD) to address the seismic safety deficiencies of San Clemente Dam (SCD) at River Mile[1] 18.6 on the Carmel River in Monterey County.  DWR and the U.S. Army Corps of Engineers (USACE) prepared a Final Environmental Impact Report (EIR) and Environmental Impact Statement (EIS) in January 2008 for the “San Clemente Dam Seismic Retrofit Project” that evaluates a number of alternatives including buttressing the dam and removing the dam.  A dam removal and channel re-routing alternative is preferred by the National Marine Fisheries Service (NMFS), which is pursuing funding and design for this alternative, with the support of the California State Coastal Conservancy (SCC).  These two groups hope to have the funding, plans, and permits in place to begin removing SCD no later than 2010.  If this alternative is developed, the Monterey Peninsula Water Management District (District) will need to relocate its steelhead counting station that is located on the SCD fish ladder.   Presently, there are no specific plans by the project proponents to provide a replacement counting mechanism as part of the dam removal project.  The project proponents have, however, indicated tentative support for creating an artificial “hard point” at the top of the re-routed Carmel River channel, as part of the final project design.  An alternative fish counting station or device could be installed at this hard point.  The current location of the fish counting station at SCD is ecologically suboptimal, as it is far enough upstream that it may count only 50% to 60% of the actual total run.  A more optimal replacement fish counting site should be established as far downstream as possible to enumerate more of the annual Carmel River run of steelhead. 





To recommend to the District’s Board the most appropriate technical solution to replace the combined mechanical fish counter and back-up digital camera currently used to count upstream migrant steelhead moving through the ladder on SCD, if the dam and its ladder are removed as part of the “San Clemente Dam Seismic Retrofit Project”.


Section 1:   Range of Conceptual Approaches for Enumerating Steelhead Run Size


Johnson and others (Johnson et al., 2007) reviewed six currently acceptable methods of enumerating the annual run size of adult salmonids, including steelhead.  These six methods fall into two general types: (1) roving surveys that must be conducted throughout the watershed, and (2) fixed sampling at a single location low in the watershed.  Roving surveys include visual surveys throughout the watershed for spawning adults or their redds (i.e., spawning nests), and mark-recapture surveys of fish carcasses left in the river throughout the watershed.  Fixed location sampling includes: (1) fixed visual surveys of passing adults from towers placed adjacent to the river at one location, (2) fish trapping weirs that temporarily block adult migration, and (3) various hydroacoustic technologies that detect and enumerate moving objects within the path of their sound beam.


Visual surveys: Visual surveys in the Carmel River would be ineffective due to the large fraction of time that flows are too turbid to view any passing fish.  Fish counting towers are used in specific streams of the Pacific Northwest, British Columbia, and Alaska, where clear runoff predominates across a wide range of flows and the channel is broad and shallow.  In these environments, an observer or a monitoring camera can be sure of detecting most of the passing fish.  These conditions rarely occur in the Carmel River and for only short periods of time during a small fraction of the migratory season.  While District staff spend one week a year conducting redd surveys in the Carmel River mainstem from SCD to Highway 1, these surveys occur only once near the end of the migratory season and are intended to identifying spawning distribution, potential low- flow barriers to fish migration, and inter-annual variation in spawning success below SCD.  In order for these surveys to be upgraded to a level in which they would be useful as a replacement for the SCD ladder count, staff would need to conduct them at least three to four times a year throughout the entire watershed below Los Padres Dam (LPD).  This effort would require access to private land in the tributary streams and hiring additional staff or contractors.  For these reasons, all visual survey approaches were eliminated from further consideration.


Mark-recapture surveys:  Mark-recapture surveys of salmonid carcasses are used throughout the Western United States to make statistical estimates of run sizes.  However, carcass surveys may underestimate total run size.  In addition, the District’s existing redd survey and fish rescue crews observe few steelhead carcasses in the Carmel River mainstem on an annual basis.  Thus, too few carcasses are observed each year to conduct a statistically valid survey.  The fact that few carcasses have been observed is likely due to a number of factors including the small size of the run, the number (possibly 20% or more) of the adult steelhead that return to the ocean, the flashy nature of the Carmel River’s peak flows that may distribute carcasses into adjacent riparian habitat where they are not observed, and the rapid removal by scavenging birds or mammals.  Even if the run size increased to the level at which carcass surveys would be statistically valid, it would still pose problems similar to those of visual surveys, i.e., access to private land (both streambed and adjacent inundation zone), multiple survey passes throughout the watershed, and hiring of additional seasonal personnel.  For these reasons, a mark-recapture carcass survey was eliminated from further consideration.


Consequently, given these constraints, only weirs and hydroacoustic technologies were considered.  Either approach is worthwhile for the District to pursue, regardless of the time before SCD and its fish counting station are removed.  In fact, even if SCD is not removed, consideration of a new location downstream that enumerates the majority of the adult run of Carmel River steelhead is justified.  Specifically, a downstream counter would provide more complete information regarding the recovery of the run under the Federal Endangered Species Act (ESA), and would help quantify the effect of remedial actions that may be required by the State Water Resources Control Board (SWRCB).  If the District chooses to pursue a replacement or supplemental fish counting station low enough in the river to enumerate most of the Carmel River steelhead run, there is a significant possibility of cost sharing or grants from State or Federal resources agencies to purchase the initial hardware for either approach.



Section 2:   Benefits and Drawbacks of the Two Approaches in the Carmel River


The use of both resistance board weirs and hydroacoustic technology to enumerate the run sizes of anadromous fish, specifically salmonids (including steelhead) is common in the Pacific Northwest, British Columbia, and Alaska.  Resistance board weirs and various hydroacoustic technologies have been utilized in Alaska since the early 1990s and 1970s, respectively.  However, the application of these approaches to the streams and rivers of California has only occurred recently, and these technologies are not in wide use.  Two recent reports summarize the results of applying these approaches to salmonids, including steelhead, in waters of the Sacramento and San Joaquin Valleys. 


Anderson and others (Anderson et al., 2007) reviewed the latest available year of results (2006-2007) from a resistance board weir installed in the lower Stanislaus River, a major tributary to the lower San Joaquin River in Stanislaus County.  Resistance board weirs are structures installed in rivers to strain flow and block upstream passage by adult fish.  The weirs force the fish into a trap where they are manually or mechanically counted.  An example of a small resistance panel weir on Scott Creek in Santa Cruz County is shown in Figure 1.


The Stanislaus River weir has been installed annually for five years since the 2002-2003 migratory season.  Periodic reports and photographs of the last two years of the weir’s installation from 2006 and 2007 are available on the Internet from Cramer Fish Sciences (Cramer), who were contracted by the U.S. Fish and Wildlife Service (USFWS) Anadromous Fish Restoration Program to set up, run, and test the weir.  Cramer’s approach used an infrared and digital camera to document fish passing through the weir’s fish trap.  In addition, Cramer trapped live fish at lower flows to take other samples from them.  The weir was considered an operational success in 2006-2007 at flows from 400 to 1,500 cubic feet per second (cfs).  This range is less than the range of flows that could be expected on the Carmel River because the Stanislaus River is a much larger river and its flows are fully regulated by multiple dams.  Discussions with the project leader indicate that the same weir design can be applied to the expected range of winter and spring flows in the Carmel River watershed (i.e., from 200 to 3,500 cfs), if a suitable installation site can be identified.


Johnson and others (Johnson et al., 2006), reviewed the results of a short-term installation of both DIDSON (dual-frequency identification sonar) and split-beam hydroacoustic technologies on Mill Creek, an important tributary to the upper Sacramento River in Tehema County.  DIDSON technology uses a sound wave projected across a river from a device mounted on the bank or a bridge abutment. The sound wave detects and recognizes passing fish.  A signal is generated and interpreted by computer software and stored on a hard drive.  The device can also produce a low-resolution black and white picture of the fish.  An example of the DIDSON mount with sonic signal generator and receiver on Scott Creek in Santa Cruz County is shown in Figure 2. 


USFWS’s Anadromous Fish Restoration Program also funded this evaluation that found DIDSON technology to be more effective than split-beam hydroacoustic technology, and appropriate for enumerating run size and timing of spring-run Chinook salmon on Mill Creek.  Evaluations were conducted at flows from approximately 100 to 5,500 cfs.


A comparison of the District staff’s opinion of the benefits and drawbacks of each counting technology as applied to the Carmel River.


Section 3:   Optimal Site Selection


A new sampling site downstream of Potrero Creek (e.g., Rancho San Carlos Road Bridge at RM 3.86) would allow a counting station to enumerate nearly the complete annual run of steelhead in the Carmel River Watershed.  Even a site as far upstream as Schulte Road Bridge at RM 6.70 would enumerate the majority of the run, whereas a counting station at Highway 1 Bridge at RM 1.09 enumerate the entire run.


Moving or adding a fish counting site 12 miles downstream from its current location at SCD will allow the District to more completely and accurately document improvements in the Carmel River steelhead run size.  Incremental increases in the steelhead population are likely to result from ongoing fish rescues, habitat improvement projects, and the re-watering of the lower Carmel River.  These improvements will primarily affect the river and run size below SCD.  Accordingly, adult steelhead counts from the lower Carmel River are needed to ensure that improvements to Carmel River habitat are not under represented in the future.


While neither the DIDSON nor the resistance board weir hardware is difficult to install, site selection for a stable channel that the DIDSON can effectively scan, or where the panels of the resistance board weir can be effectively anchored, is critical for reliable measurements.  In this regard, it is not known if any private landowner will allow annual access to their property to install and maintain a large resistance board weir.  It is more likely that a private landowner, the County of Monterey, or the California Department of Transportation (CALTRANS) will allow installation of a DIDSON on or adjacent to a bridge abutment. 


It would be best for the District to employ a consultant experienced with installing either technology in unregulated rivers to guide its employees in choosing an installation site and completing the first season’s installation.  Doing so is likely to greatly enhance the success of the project and reduce the degree of adaptive management needed to implement any new approach.   



 Section 4:   Recommended Course of Action


Due to hydrologic and hydraulic conditions in the Carmel River Watershed, only two approaches for a new station to count immigrating adult steelhead appear feasible.  Both will cost approximately $150,000 to implement in the first year, and each has its drawbacks and benefits.  I believe the most non-intrusive, cost effective, and reliable approach is use of a DIDSON monitoring station.  This technology is being used for this purpose on a wide variety of fish species throughout the world, and on salmonids in the Pacific Northwest, British Columbia and Alaska.  However, since there is no long-term DIDSON installation in California on a river similar to the Carmel River, I recommend a test installation and pilot study be done during the expected peak of next year’s steelhead run in the first week of March 2009 to prove the technology’s utility in the Carmel River Watershed.  If this test is successful, the District should proceed to budget for a permanent installation in Fiscal Year 2009-2010, and apply for State or Federal matching grants to subsidize the hardware costs.  Installation should proceed as soon as feasible so that as many years of paired data can be collected at the new and existing fish counting locations, before SCD  is removed.



Section 5:   Conclusions


The District should consider including up to $20,000 in the Fiscal Year 2008-2009 Mid-Year Budget adjustment for a pilot installation of DIDSON fish counting technology in the lower Carmel River Valley, during March 2009.  Pending the outcome of the pilot study, the District should prepare to budget approximately $150,000 and apply for grants for a permanent installation of either the DIDSON technology or a resistance board weir and fish counting station in Fiscal Year 2009-2010.










Table 1.

Factors Affecting the Benefits and Drawbacks of Two Alternative Steelhead

Counting Technologies Applicable to the Lower Carmel River





Weir and Trap Station


Estimated Initial Installation Cost


$125,000 - $140,000

Estimated Annual Re-Installation Cost



Estimated Annual Maintenance Cost



Staff Positions Required For Installation

2-Biologists & 4-Technicians

1-Biologist & 1-Technician

Days Required For Installation/Removal



Staff Positions Required For Operation

1-Biologists & 2-Technicians


Minimum Ongoing Staff Allocation

21 person-days, weekly

1 to 3 person-days, weekly

Estimated Annual Operational Staff Costs


~$4,000 - $17,000

Site Footprint



Degree of Access Required

Large & Daily

Small & Intermittent

Probability of Acquiring Access



High Flow Failure Risk



High Flow Loss Risk



Coverage Across All Predictable Flows

Most, But Not All Flow Levels

At All Flows But Not All Depths

Complexity of Environmental Permitting



Would Require ESA Section 10 Permit



Would Require DFG 1600 Permit



Would Require MPWMD or Monterey County Permits



Cost of a Pilot Study

Similar To Installation

Less Than Full Installation

Liability Risk of Installation/Operation



Risk of Vandalism



May Enhance Opportunity For Poaching















Figure 1.


Example of a Small Resistance Panel Weir on Scott Creek in Santa Cruz County





















Figure 2.


Example of a DIDSON Mount with Sonic Signal Generator and Receiver

on Scott Creek in Santa Cruz County




















References Cited


Anderson, Jesse T., Cark B. Watry, & Ayesha Gray.  2007.  Upstream Fish Passage at a Resistance Board Weir Using Infrared and Digital Technology in the Lower Stanislaus River, California.  33pgs.  Cramer Fish Sciences, 636 Hedburg Way, #22, Oakdale, CA 95361.  (209) 847-7786

[Available on the Internet at: http://www.fishsciences.net/reports/index.php]


Cramer Fish Sciences.  2007.  Stanislaus River Weir Project: E-mail Summaries. Twenty-one periodic progress reports on two years of weir operations from 2006-2007 at: http://fishsciences.net/postcards/postcards.htm.  [Source of the photographs of the Stanislaus River Weir.]  Cramer Fish Sciences, 636 Hedburg Way, #22, Oakdale, CA 95361.  (209) 847-7786


Johnson, David H., Brianna M. Shrier, Jennifer S. O’Neil, John A Knutzen, Xanthippe Augerot, Thomas A. O’Neil, and Todd N. Persons.  2007.  Salmon Field Protocols Handbook: Techniques for assessing status and trends in salmon and trout populations.  478 pgs.  American Fisheries Society, Bethesda, Maryland.


Johnson, Peter, Bryan Nass, Don Degan, James Dawson, Mathew Johnson, Brenda Olson, & Colleen Harvey Arrison.  2006.  Assessing Chinook Salmon Escapement in Mill Creek Using Acoustic Technologies in 2006.  46 pgs.  United States Fish & Wildlife Service (USFWS), Anadromous Fish Restoration Program, Dept. of the Interior, 10950 Tyler Rd., Red Bluff, CA 96080



Scientists and Experts Consulted


Anderson, Jesse T.  2008 . Personal Communication.  Phone conversation on or about 03//08 about his experiences operation the resistance board weir on the Stanislaus River.  Cramer Fish Sciences, 636 Hedburg Way, #22, Oakdale, CA 95361.  (209) 847-7786

Dorsey, Jeanne.  2008.  Personal Communication.  Phone conversation on 6/6/08 about the applicability of DIDSON technology to conditions in the Carmel River.  Ocean Marine Industries, Inc., 2810 Hudson Street, Chesapeake, VA 23324.  (757) 382-7616  Vendor for Sound Metrics: http://www.soundmetrics.com/index.html

Hayes, Sean.  2008.  Personal Communication.  Site visit to his resistance board weir installation on Scott Creek on Monday, 3/31/08.  [Source for photographs of the resistance board weir installation on Scott Ck.]  National Marine Fisheries Service (NMFS), Fisheries Ecology Division, Southwest Fisheries Science Center, 110 Shaffer Road, Santa Cruz, CA 95060-5730.  (831) 420-3937


Johnson, Peter.  2008.  Personal Communication.  Phone conversation on 6/6/08 about the applicability of DIDSON technology to conditions in the Carmel River.  LGL Limited, environmental research associates, 72 Cascade Mall Dr., P.O. Box 225, N. Bonneville, WA 98639.  (509) 427-4862.  http://www.lgl.com/


Pipal, Kerrie.  2008.  Personal Communication.  Site visit to her DIDSON installation on Scott Creek on Monday, 3/31/08.  [Source for photographs of the DISDON installation on Scott Ck.]  National Marine Fisheries Service (NMFS), Fisheries Ecology Division, Southwest Fisheries Science Center, 110 Shaffer Road, Santa Cruz, CA 95060-5730.  (831) 420-3935







[1] River Miles (RM) are measured from the river mouth, i.e., 0.0 mile, and increase as you move upstream.