Authorizations and Permits for Protected Species (APPS)

The indigenous, anadromous fish populations of California's Central Valley have been severely reduced due to a variety of man-caused alterations to the environment. The region's anadromous fish populations have been extirpated from most of their historic range and the existence of the few remaining depleted populations are continually challenged.  Diversions and bypasses such as the Colusa Basin Drainage Canal (CBDC) and both Fremont and Tisdale weirs affect immigration and emigration cues for anadromous fish. With escapement numbers of Sacramento River winter-run Chinook salmon measured in the thousands, any loss to the spawning population is significant.  Further, reduced flows and higher water temperatures in the upper Sacramento River associated with extreme drought conditions may lead to substantial losses to both incubating eggs and emergent fry. These losses occur through lethal water temperatures or standing as a result of reduced flows.  Sacramento River flow management decisions are often the cause of stranding in this section of the river and management of flows is the best way to avoid the need for fish rescues and relocation. In order to circumvent potential losses and contribute towards the continued existence and recovery of the sole remaining population of the endangered Sacramento River winter-run Chinook salmon evolutionary significant unit (ESU), CDFW has identified the following rescue and relocation activities that may be carried out depending on environmental conditions.

Wallace Weir Trapping and Relocation Operation
The previously un-diagnosed stranding of winter-run Chinook salmon in the CBDC and the ongoing potential for entrainment of ESA-listed salmonids and SDPS green sturgeon behind flood relief structures, if fixed, could be a substantial advancement to enhancing the spawning populations. Attempts will be made to trap and relocate adult Chinook salmon and other species of management concern before they enter and become entrained within the CDBC. Wallace Weir within the Yolo Bypass has been identified as a potential entry point into the CBDC.  On June 20, 2016, NMFS completed a Section 7 Consultation and issued a biological opinion to the U.S. Army Corps of Engineers (USACE) for the Wallace Weir Fish Rescue Project (WCR-2016-5014), which involves construction of a new, permanent weir with a flow control structure, installation of a positive fish barrier (i.e., picket weirs), construction of an access road and bridge across the new weir and a control building for the new flow control structure, demolition of the existing weir, and construction of a permanent fish rescue facility to replace the temporary fyke trap previously used for fish collection (authorized under Permit 18181-2M). Although the biological opinion issued to the USACE authorizes the construction activities outlined above, it does not authorize the rescue and relocation of ESA-listed salmonids and SDPS green sturgeon at the new fish trapping facility. Operation of the new fish collection facility for purposes of collecting, handling, and transporting captured fish is proposed under Permit 18181-3A.  

Wallace Weir Fish Rescue Program Objectives:
1) Collect and relocate Target Species that become entrained at the fish collection facility at Wallace Weir.
2) Record and report numbers and species composition of trapped fish and maintain a program database.
3) Mark and/or tag Target Species collected at the facility and collect genetic samples.
4) Refine fish rescue methods to minimize handling stress and costs of operations.
5) Document the magnitude of stranding of Target Species and to the extent possible document survival and spawning success of fish through mark and recapture methods and acoustic tracking.
6)Document any weir over-topping resulting in the potential for fish to move into the CBDC. This will be used to inform the need for potential rescues in other areas of the CBDC watershed.

Rescue and Relocation associated with Sacramento River Flood Control Project Weirs and Flood Relief Structures – Tisdale and Fremont Weirs
Both the Sutter and Yolo bypasses will be surveyed after high flow events with a specific focus on Tisdale and Fremont weirs in the Sacramento River (see attached document; CDWR 2010, Flood Operations Branch, Fact Sheet Sacramento River Flood Control Project Weirs and Flood Relief Structures). During high flow events a significant proportion of the Sacramento River is diverted into the Sutter and Yolo Bypass through specific flood relief structures. Substantially more water can be passing through the bypasses than is in the river itself during these flood events. This dramatically alters not just the volume of water in the main channel but the variations in flow over time. Fish in the river downstream of these flood relief structures experience a drastically different flow regime then fish do upstream of these structures. This can affect immigration and emigration cues for anadromous fish. Adult fish migrating upstream may be attracted into the bypasses. Additionally, during high flows that overtop the flood relief structures (weirs), a large percentage of out-migrating fish in the river may be diverted into the bypass. As flows recede many of these fish can then become stranded in the bypasses. This has implications on detectability of fish moving past in-river monitoring sites and is of special concern when tracking movement of listed stocks. More importantly entrainment and stranding can result in significant mortality for fish including listed species.  Rescue efforts provide an invaluable opportunity to save stranded fish while learning from them.  Because each stranded individual would parish in the absence of intervention, data collection for this study can be viewed as information gathered from salvaged specimens (see description of Salvage Specimens in NOAA Tech Memo NMFS-OPR- 45, March 2010, pg. 48). It is crucial to identify the level of impact flood relief structures and diversions are having on populations of listed species and to identify whether stranded fish can successfully contribute to the population after being rescued. Information from this study has management implications for water project operations.

Upper Sacramento River Redd Dewatering Surveys and Rescue of Stranded Juvenile Winter-run Chinook Salmon 
Beginning in 2013 an effort has been made by the fisheries agencies to annually monitor winter-run Chinook salmon redds. Monitoring includes: searching for, identifying, marking, and repeated measuring of winter-run redds found in shallow water. This monitoring allows CDFW biologists to predict the flow at which redds will be dewatered on a redd-by-redd basis. Given this knowledge, it is possible to physically modify redds in danger of being dewatered to lessen the impacts to emerging juveniles in each redd.  Ideally, Keswick releases would be managed to protect winter-run redds from dewatering.  Unfortunately, the unprecedented drought has reduced Shasta storage to historic lows, leaving little flexibility for reservoir releases and the protection of salmonids.  

CDFW understands that the ideal situation is not to disturb Chinook salmon redds at all.  However, in case of dewatered redds, the disturbance is justified as an attempt to provide as much opportunity for survival as possible while minimizing disturbance. As redds become dewatered, the top of the redd emerges from the water preventing emergent fry from exiting through the top of the redd.  Further, the water velocity around the remaining redd area is typically reduced, resulting in less flow through the redd. This can trap emerging fry, preventing them from departing the underwater sides of the redd and reducing available dissolved oxygen and raising water temperatures. Removing existing substrate from the top of dewatered redds will produce more flow over and through the redd, and theoretically, allow for fry emergence and passage to the surrounding river.

Reduced flows not only affect incubating eggs and emergent fry.  Juvenile salmonids can become stranded when reduced flows from Keswick Dam result in isolated pools or channels which were previously connected (allowing free passage) at higher flows to the Sacramento River.  Stranding can lead to direct mortality when these areas drain or dry up. Indirect mortality can result through increased susceptibility to predators (otters, raccoons, birds, etc.) or water quality deterioration (increased water temperature, reduced dissolved oxygen, etc.) in shallow or stagnant stranding locations (Jarret and Killam 2014). CDFW agrees that the ideal situation is to leave fish undisturbed unless there is a high likelihood that the stranding site would not be reconnected with the stream in the immediate future.

Fish rescues will also be conducted in Shasta and Tehama counties including but not limited to the following locations: Sacramento River, Deer Creek, Mill Creek, Antelope Creek, and various urban streams.  Fish rescues may also occur on other Sacramento River tributaries but are not anticipated on a regular basis as those mentioned above.

Objectives are to: 
1) Capture, tag and relocate Sacramento River winter-run Chinook salmon and other species of management concern in the lower reaches of the CBDC at Wallace Weir within the Yolo Bypass.
2) Construct and place modified fyke traps at key locations within the interior of the CBDC system to capture, tag and relocate stranded fish if fish passage occurs at the Wallace Weir Trapping Facility.
3) If environmental conditions (high flows, flooding) warrant monitoring and rescue of fish entrained behind Fremont and Tisdale weirs, CDFW aims to assess the level of entrainment and evaluate the survival and behavior of entrained adults that are rescued and relocated.
4) Monitor winter-run Chinook salmon redds by identification of redds at risk of being dewatered, marking of redds, and repeated measurements of water levels around redds. This monitoring allows CDFW biologists to predict the flow at which redds will be dewatered on a redd-by-redd basis. 
5) If deemed necessary, CDFW may physically modify redds in danger of being dewatered to lessen the impacts to emerging juveniles within each redd.
6) Survey known stranding sites immediately following Keswick Dam flow reductions (as feasible), to determine if a fish rescue is necessary.  
7) Conduct fish rescues in Shasta and Tehama counties including but not limited to the following locations: Sacramento River, Deer Creek, Mill Creek, Antelope Creek, and various urban streams as needed.
8) Identify conditions resulting in high levels of entrainment specific to each location.

During high flow events a significant proportion of the Sacramento River is diverted into the Sutter and Yolo Bypass through specific flood relief structures. Substantially more water can be passing through the bypasses than is in the river itself during these flood events. This dramatically alters not just the volume of water in the main channel but the variations in flow over time. Fish in the river downstream of these flood relief structures experience a drastically different flow regime then fish do upstream of these structures. Furthermore, agricultural diversions and drainages take Sacramento River water and send it through a maze of canals, ditches, and natural streams down the heart of California's Central Valley, from as far north as Glenn County, and drain it back into the Sacramento River just a few miles from where it branches off from the confluence of the San Joaquin River. The main structure running the length of the agricultural area is the CBDC. This influence of Sacramento River water can cause migrating salmon to stray into waterways that are not conducive to spawning or have no easy returns to the River. 

Significant reductions in flow also have the potential to entrain salmonids. Stable and continuous river flows are important to the early life history (egg incubation to emergence from the gravel) of salmonids. If redds are dewatered or exposed to warm, deoxygenated water, incubating eggs/larval fish may not survive. After emergence from their redd, juvenile salmon can become stranded in shallow isolated water and be exposed to the same poor environmental conditions as well as increased predation. For the eggs and juveniles to survive they need water, of a suitable temperature, velocity, and water quality, at all times. Juvenile stranding surveys are implemented to observe and report on locations that could potentially contain stranded salmonids that are isolated to varying degrees by flow reductions. Attempts will be made to capture and relocate stranded juveniles to more suitable habitat.  Further, CDFW will assist with the emergence of stranded fry in redds at risk of being dewatered. This effort should be considered as a last resort to increase the opportunity for juvenile Sacramento River winter-run Chinook salmon to emerge from a redd that IS going to be dewatered by flow reductions.

Recovery and Relocation of Fish Entering the CBDC at Wallace Weir Fish Facility
Wallace Weir is located at the terminus of the Knights Landing Ridge Cut and the west levee of the Yolo Bypass, approximately three miles north of Interstate 5 and five miles northeast of the City of Woodland. The new permanent structures associated with the new Wallace Weir Fish Facility will improve flow control for agricultural purposes and function to rescue fish for relocation to the Sacramento River. CDFW's rescue and relocation efforts to date have provided an understanding of timing and magnitude of potential fish entrainment and loss, as well as conditions that can exacerbate the potential for fish entrainment. These efforts have also allowed for methods and protocols to be developed and refined that minimize handling stress and lethal take of ESA-listed species during rescue efforts.

CDFW will check the fish collection facility at Wallace Weir on a daily basis or more frequently if necessary. The facility will impound all fish species, so all fish present will be handled and removed from the fish collection facility. Target Species and Species of Management Concern will be prioritized for collection, processing, transportation, and release back to the Sacramento River. The Sacramento River release location(s) will be evaluated and may vary with species and time of year, but will only occur in locations where CDWR or CDFW have property rights or landowner permission to carry out fish releases. All salmonids and sturgeon will be identified to species, measured and evaluated for condition and sexed if possible. To document the magnitude of stranding of ESA-listed fish, genetic samples will be collected from all salmonids. To allow information to be gathered on movement, survival, and spawning success after releases, salmonids and sturgeon that are rescued will be marked and/or tagged. Species other than Target Species or Species of Management Concern that are found in the facility will be passed through to the upstream or downstream side of the weir using infrastructure incorporated into the facility.
 
Potential Rescue/Salvage in the upper CBDC 
If and when fish passage is thought to occur (in the unlikely event that the trapping facility experiences operational issues), CDFW will initiate a roving survey using dual identification sonar (DIDSON) imagery at known choke points within the CBDC and associated tributaries to look for focal species. Sonar imagery will help to identify substrate complexity, species presence/absence, and potential capture equipment needed for a rescue. Sonar imagery will also be helpful in identifying underwater hazards that may foul capture gear or be dangerous for CDFW personnel to work near.

Once focal species are determined to be present at any one location in the CBDC, CDFW will focus efforts to capture and then relocate wayward fish to the Sacramento River. Semi-permanent barriers and fyke traps may be installed upstream in key areas within the CBDC such as, but not limited to, the CBDC diversion structure at the juncture of Hunter Creek, under the 4 Mile Road Bridge and Dam 3 locations on Hunters Creek, Dam 1 at North Logan Creek; the confluence of Logan and North Logan Creeks, the confluence of Stone Corral Creek and Funks Creek, and the CBDC near the Delevan NWR. CDFW discovered that fish strayed to these locations during the 2012/13 season. Each rescued fish will be measured, sampled for tissues (genetic testing), tagged externally with two individually-numbered Floy tags, placed in a 350-400 gallon fish transport truck and returned to the Sacramento River at Tisdale Weir. 
 
Monitoring Entrainment and Rescue of Fish at Fremont and Tisdale Weirs
CDWF aims to identify the level of SDPS green sturgeon entrainment and stranding into Sacramento River flood relief structures and bypasses, survival and behavior of entrained adults that are rescued, and to identify conditions resulting in high levels of entrainment specific to each location. In this effort, flood relief structures will be monitored after high flow events throughout the Sacramento River. Any stranded adult sturgeon will be captured if possible using block nets and hoop nets, measured and tagged both acoustically (internal VEMCO acoustic tags) and with two colored and individually numbered Floy tags. If any adult or juvenile Chinook salmon or steelhead are found to be entrained during rescue efforts, they will be captured using beach seines, their presence will be documented. Adult salmonids will be tagged with two colored and individually numbered Floy tags. Steelhead (adults and juveniles) may also receive a PIT tag as part of CDFW's Steelhead Monitoring Program.  All rescued fish will be transported to the nearest Sacramento River location and released.

Upper Sacramento River Redd Dewatering Surveys and Rescue of Stranded Juvenile Winter-run Chinook Salmon
CDFW staff will survey known stranding sites immediately following Keswick flow reductions (as feasible), to determine if a fish rescue is necessary.  If determined necessary, CDFW staff will seine, net, or electrofish (in this order of priority to reduce negative impacts to already stressed fish) stranding locations based on staffs experience and feasibility at each location.  Fish will be enumerated by species and race (visually estimated), then immediately transported by bucket to an adjacent –river section that is not isolated. See Jarret and Killam 2014 (attached) for data collection protocols. Side channel sites (both natural and restored) may also be surveyed in order to get lengths and weights on captured Chinook salmon to calculate condition factor of fish using various restored habitats.

Winter-run redds in shallow water will be identified and monitored by boat crews to determine formation date and subsequent emergence date of each redd. These redds will be repeatedly measured to determine the depth of water column above the highest point of the redd during each river flow reduction. When a redd is in jeopardy of becoming dewatered, (based on the redd depth and the schedule of flow reductions) CDFW may take action to reduce the impacts of dewatering. Just prior to a Keswick flow reduction (1-2 days), if deemed necessary, a field crew will gently remove substrate from the tops of redds that are likely to become dewatered (e.g. redds in water 2-3 inches or less before a 250 cfs reduction). Crews can attempt to remove by hand the rocks from the tops of redds to a sufficient depth that will allow water to remain freely flowing over the redd top after the forecasted flow reduction. Redd tops will be removed using a slow and gentle manner to minimize abrasion impacts to fry in the uppermost area removed. Water velocity will be measured at the redd before and after the substrate removal process. Water depth measured from the redd top to the water surface will also be recorded pre and post rock removal. Photographs will document the substrate removal process. Numbers of fry observed during the redd removal will be noted. Crews will revisit and repeat if necessary on the monitored redds until after the emergence date of each redd in the effort has passed.

If any redds become entirely dewatered, CDFW staff may remove rocks and dig up redd to determine the level of mortality that occurred as a result of dewatering the redd. It is important to document whether there is significant mortality occurring as a result of flow reductions and changes in water operations in the upper Sacramento River.

Upper Sacramento River Basin Tributaries 
Fish rescues will also be conducted in Shasta and Tehama counties including but not limited to the following locations: Deer Creek, Mill Creek, Antelope Creek, and various urban streams.  Fish rescues may also occur on other Sacramento River tributaries but are not anticipated on a regular basis as those mentioned above. 

Water diversion structures along various creeks and tributaries to the Upper Sacramento River have the potential to entrain ESA-listed salmonids. Although screened, these diversions have not been equipped with fish bypass return structures. When these diversions are operated in the spring, out-migrating juvenile Chinook salmon, juvenile steelhead, adult steelhead kelts, and other fish are drawn into the ditches and are trapped between the diversion head-gates and the fish screens.  Once entrained, these fish must be manually captured and released downstream of the diversion or they will succumb to predation or lethal summer water temperatures.

The capture method will primarily be beach seining.  When seining is not feasible other methods such as fyke netting, backpack electroshocking or hook and line may be used as a last resort.  If necessary, a one-ton flat-bed truck fitted with a 200 gallon oxygenated water tank will be used to transport rescued salmonids.  If staff find a suitable release location nearby, fish may be relocated by hand (aerated buckets) to avoid transportation by truck. Rescued fish will be relocated and released at the Sycamore Boat Launch downstream from the Red Bluff Diversion Dam (RM 243) or the nearest suitable release location on the Upper Sacramento River.