Authorizations and Permits for Protected Species (APPS)

Steelhead population in the SJR was extirpated; however, small populations of steelhead persist in the lower SJR tributaries (i.e., the Stanislaus and Tuolumne Rivers and possibly the Merced River) and in the Calaveras River.  Monitoring of steelhead in the SJR and its tributaries is especially challenging due to extremely low abundance. Steelhead populations are depressed to the point where monitoring opportunities are limited because sample sizes are too low to use statistical analyses, and depressed to the point that even determination of presence is difficult. Steelhead are currently extirpated from all waters upstream of the Merced-SJR confluence. NMFS has concluded that populations of naturally reproducing steelhead have been experiencing a long-term decline in abundance throughout their range.  Populations in the southern portion of the range have experienced the most severe declines and stocks in California has been particularly steep.  Please refer to the 2014 Steelhead Monitoring Plan Report and SJRRP Programmatic Biological Assessment for more information. No steelhead were observed during 2012–2014 SJRRP Steelhead Monitoring efforts.
The San Joaquin River historically supported large runs of spring-run Chinook salmon. Completion of Friant Dam and reduced flows into the mainstem SJR dried up downstream river sections. By 1950, the entire run of spring-run was extirpated.  To facilitate reestablishment of spring-run Chinook Salmon within the SJRRP, juvenile spring-run were released in 2014 and 20154 as an experimental population.  It is anticipated that these fish could begin returning to the SJR as adults during the spring of 2017. Monitoring and translocation of these returning fish is needed as in-river barriers exist. Steelhead monitoring from January–April will serve as a means to monitor early returning adult spring-run Chinook salmon.  No spring-run Chinook salmon adults were observed entering the Restoration Area during the 2016 monitoring efforts

Migrating adult steelhead are difficult to monitor with commonly used salmonid monitoring techniques (e.g., carcass surveys, snorkel surveys, redd counts) due to their unique life-history traits.  Steelhead, unlike salmon, may not die after spawning.  Therefore, carcasses may not be available for a mark- recapture survey.  In addition, steelhead migrate and spawn during the late-fall, winter, and spring months when rivers have periods of pulse flows (e.g., Vernalis Adaptive Management Plan, Merced River pulses), high flows (e.g., flood releases), and turbid water conditions.  The following sampling methods will be used for the CV steelhead monitoring plan:

Electrofishing– Electrofishing is a common method used in monitoring steelhead populations (e.g., Mill and Deer Creeks, and Feather, American, Mokelumne, Stanislaus, and Merced Rivers).  One potential drawback from electrofishing involves the difficulty in obtaining permits due to the possibility of injuring anadromous salmonids (Eilers 2008).  However, electrofishing effectiveness and safety have improved over time (Bonar et al. 2009).  Design specifications to reduce injury to fish, and a comprehensive review of electrofishing literature can be found in Snyder (2003).

Sampling will be completed from December–April annually after the Hills Ferry Barrier is removed and adult fall-run trap and haul has ceased.  Repeated capture of resident fish (non-steelhead) is anticipated, thus intervals between sampling periods will help provide recovery time from sampling and handling stress. Electrofishing methods will follow NMFS guidelines for sampling waters with anadromous fish (NMFS 2000).  However, stated guidelines were for backpack electrofishing, though steelhead monitoring biologists and were not precluded from boat electrofishing.  A Smith-Root 5.0 GPP raft-mounted electrofisher (Smith Root, Vancouver, WA) will be used during this time using the following settings:  pulsed direct current, voltage range set at 50-500 V, with a power output range of 10-60%, and cycle frequency from 15–60 Hz.  Settings will be determined by water conductivity and adjusted to maximize capture efficiency while minimizing electrical exposure (i.e., lowest setting required to elicit response without extended shocking times).  Sampling sites will include: Mud Slough, Salt Slough, Newman Wasteway, Eastside Bypass, Mariposa Bypass, Sand Slough Control Structure, and the base of Sack Dam.  

Fyke Nets– Fyke nets will be used to survey for upstream migrating steelhead.  Fyke nets are constructed of 2.4-cm square #252 knotless nylon netting formed over 5 consecutive 1.2-m hoops and a 1.2-m square, welded-conduit frame entrance.  The traps contain 2 throats with a 25-cm diameter opening.  Wings walls, attached to the sides of the net opening, are 1.2 m deep and long enough to span the river (max wing length 30.5 m), with small floats spaced every 61 cm on top, and a lead line on bottom.  Nets are held in place with anchored t-posts.  The net entrances face downstream, with the wing walls extending to shore in a v-shaped pattern.  Fyke nets will be deployed in sampling locations, but not limited to, upstream of the confluence of the Merced River, mainstem San Joaquin River, mouths of Mud Slough, Newman Wasteway, and existing structure at Sack Dam.  This proposed technique will be implemented once the Hills Ferry Barrier is removed around mid-December and may remain deployed until the end of April.  Marker buoys will be placed up- and downstream of each fyke net, and flashing amber lights and visibility tape will be affixed to the net and wing walls to alert boaters of the net's presence.  Daily checks will take place to reduce the likelihood of injuring fish. Sampling occurring from February through April 2017 will be used to supplement the pilot adult spring-run Chinook Salmon monitoring being conducted by the U.S. Fish and Wildlife Service using a v-shaped net paired with a Vaki Riverwatcher Unit near Hills Ferry (10a1A permit #17781).  

Trammel Nets– Trammel nets are most commonly used as stationary gear to block off channels with low velocities or no flows.  The nets consist of three parallel vertical layers of netting; the inner net has a smaller mesh size (small hole spacing to prevent steelhead from becoming gilled), while the outer nets have mesh size large enough for fish to pass.  The larger and smaller mesh size nets form a pocket when fish try to swim through. A buoyant top line and weighted bottom line keeps the trammel net oriented vertically in the water column.  Brightly colored buoys will be attached to the terminal ends of the net to alert boaters and other recreationists to the nets and avoid entangling themselves, their boats, or their fishing gear. Trammel nets range in size from 0.9-1.8 m (3-6 ft.) tall and 11.4-30.5 m (37.5–100 ft.) long. Trammel nets will be continuously monitored and set for a maximum period of 4 h.  Trammel nets may also be employed during high velocity flows, manned during the entire time of their deployment, and their drift cycle will be limited to 10 minutes.  To ensure the safety of steelhead, fisheries biologists tending the nets will follow at a close distance to observe risk of entanglement, and respond quickly to retrieve the nets.  Sampling time will depend on the number of fish and bycatch caught at each location.  Capture of the same fish multiple times is to be anticipated, thus monthly sampling is important to ensure fish recovery from stress between captures.

Seine - When electrofishing or fyke netting cannot be effectively used to capture steelhead, a hand seine will be used to safely collect fish.  This would be the primary means for collecting fish below a passage impediment or potentially entrained in a small canal or pool in shallow water, as seines are often used to capture adults for rescue/relocation.  Seines for steelhead monitoring will be constructed of 1/2-inch nylon knotless mesh, hand tied to a 5/16-inch hollow-braided polypropylene rope with 4-inch floats every 24 inches on top, and #10 leads every 12 inches on the bottom.  These nets are 6 foot tall and 75 feet long.  However, seines of various lengths and mesh sizes will be used depending on location, flows, river conditions, and size of target fish.  Mesh size will be decreased for juvenile salmonids and knotted mesh should never be used as it has abrasion risks.

The pattern of seining and seine size will depend on the structure of the pool to be seined, with a goal to ensure the best coverage of the pool without risking having the seine hang up on debris and allowing the fish to escape. Generally, the seine is deployed, circling the fish, and pulled closer the shore.  The net poles on the ends are positioned forward and the lead-line is kept snug to the bottom, as the net is pulled to shore.   Personnel seining will be careful not to seine debris in a manner that could injure fish.  The seine will be inspected in the water for listed species. Steelhead entrapped in the seine purse will be subsequently processed and removed for transport, and bycatch immediately released to the water. Steelhead captured by seine are placed in 15-gallon tub and hand-carried to the transport tank. 


 Fyke Trap

During high flood flow conditions turbidities, depths, and debris loads, may render other methods to monitor and capture CCV steelhead challenging and ineffective.  Therefore, steel fyke-traps may be deployed as an alternative to these methods under a high flow year.  Steel fyke-traps have two chambers (42-in diameter) with a reduced funnel (22-in diameter) opening between chambers, and are constructed of 2.25-in plastic coated chainmail.  These have a large internal compartment constructed of high tensile resin-infused netting, permitting capture and maintenance of adult salmonids without inadvertently causing injury or excessive stress. Traps are equipped with exclusion bars and plastic internal fykes to restrict entry and allow for escape of aquatic mammals.  Traps will be deployed upstream of the Merced River confluence, and will be checked at least once daily.  Ample boat passage will be made available, and orange buoys and flashing amber caution lights will alert river-users to the traps.

Fish Handling and Relocation– In the event that a steelhead is captured during monitoring activities, data will be collected according to the Department of Fish and Wildlife Comprehensive Monitoring Plan for Steelhead in the California Central Valley (2010).  Fish will be subjected to the following handling and transporting procedures:  Steelhead would be documented, measured (FL/TL), sexed (if possible), scale and tissue samples collected (Bagenal and Tesch 1978), checked for injuries and presence of identifying tags, and photo documented.  Additionally, fish would be PIT tagged with a unique identification number for future identification.  Captured steelhead would be transported downstream, below the SJR and Merced River confluence (near latitude, longitude: 37.350356, -120.976167).  The exact release location would be dependent on river conditions. Transport would involve water to water transfers, a 550-L transport tank, and smaller transport containers may be used for short distances (i.e. where access to the stream is limited to access by foot).   Immediately prior to transport, the tank would be filled with river water near the area of capture.  Salt (NaCl) would be added to the transport water to decrease the cellular-holding water ionic gradient as a means to minimize stress.  Steelhead would then be transferred from the river to the transport tank with a water-to-water transfer to reduce handling stress and loss of slime.  Oxygen would be supplied via compressed cylinder and micro-bubble diffusers to maintain dissolved oxygen levels near saturation.  In the instance of extended transport duration (i.e., >30 min), an inspection of the fish and transport equipment would occur after the first 30 minutes, and each hour thereafter.  Captured steelhead would be acclimated to receiving water conditions (i.e., temperature and chemical gradients) at the release location.

Lethal water temperatures for migrating adult steelhead is 23-24 °C (75°F) and thought to be higher for those populations acclimated to locations in the southern extent of their occurring range.  In order to not jeopardize steelhead that may be present, no steelhead monitoring will occur if river temperatures reach 20 °C (68 °F). However, temperatures during previous monitoring periods did not elevate beyond 18.4 °C (65 °F).  In the unlikelihood of a juvenile steelhead capture, scales and fin clip will only be collected from live steelhead when water temperatures are below 15.5 °C (60 °F).

Vaki Riverwatcher- Upstream migrating adult spring-run Chinook Salmon and Steelhead will be visually monitored continuously by a Vaki RiverWatcher in the San Joaquin River near Hills Ferry (Reach 5) from February through July.  A scanner unit will be anchored to the riverbed using steel posts and connected to two wing walls consisting of 2.4-cm square knotless nylon netting. Wing walls, attached to the sides of the scanner unit's frame, will be at least 1.2 m deep and long enough to span the width of the river, with small floats spaced every 61 cm on top and a lead line on bottom. The scanner unit and its wing walls will be held in place with anchored T-posts.  Net entrance will face downstream, with wing walls extending to shore in a v-shaped pattern. T-posts used to secure the fyke nets and wing walls, as well as weir anchor posts, will be marked with highly visible flagging, and at least one flashing light to provide visual warning cues for boaters.

The scanner unit will be connected and configured to scan and record the silhouette of each fish that volitionally passes through the wing walls and scanner unit. The scanner unit will estimate the total length of each fish passing through the unit and record the water temperature during each fish passage event. Using the silhouette of the fish, we will be able to determine if the fish is adipose clipped. All information collected by the scanner unit will be stored in a control unit powered by a deep cycle battery, which will be recharged using solar panels or a generator as needed.  The scanner unit will be checked daily throughout the sampling period to ensure stability and proper function of the equipment.  These data will be subsequently stored in and analyzed using Winari software located at the Lodi Fish and Wildlife Office.

N/A

There will likely be minimal effects associated with electrofishing, fyke and trammel netting, and the Vaki Riverwatcher on associated sampling/handling stress of steelhead.  Monitoring efforts may also delay upstream migration as temporary nets in the river due pose a short-duration migration barrier.  There should be no adverse effects on aquatic reptiles and mammals during the December–April time period.

All persons implementing SJRRP steelhead monitoring activities will be knowledgeable with the conditions of all applicable permits and requirements of the Endangered Species Act, will follow the conditions of all applicable permits, and will follow appropriate protocols to minimize injury to sampled fish and will have access to properly maintained state-of-the-art equipment.

Live steelhead shall be handled with extreme care and kept in water to the maximum extent possible during sampling and processing procedures. Adequate circulation and replenishment of water will be maintained in holding units.

When a sample is comprised of a mix of species, any captured steelhead will be processed first and removed as soon as possible after being captured to minimize the duration of handling stress.  Distressed steelhead rescued at the capture site will be allowed to recover to the maximum extent possible prior to being released into the mainstem San Joaquin River.

Each researcher using an electrofisher as a sampling technique will follow operation protocols described in the "NMFS Guidelines for Electrofishing Waters Containing Salmonids Listed Under the Endangered Species Act, June 2000" (Guidelines).  Prior to the start of electrofishing at each location, water temperature and conductivity measurements will be taken to determine the criteria appropriate electrofishing  guidance.

Fyke traps will be checked daily (every 24 hours), at a minimum, during operation.  During periods of peak migration, high flows, and/or debris levels during storm periods, traps may be checked more frequently, as needed, to minimize potential for mortality.

Trammel net drifts will be continuously monitored in the San Joaquin River.

Steelhead will not be handled if stream temperatures at the capture site exceed 20 °C (68 °F).  Under these conditions, fish will only be identified and counted.  Scales will only be collected from live juvenile salmonids when water temperatures are below 15.5 °C (60 °F).

The San Joaquin River Restoration Program maintains the staffing expertise, boats, sampling gear, access agreements, and funding to successfully accomplish the objectives and activities stated in this application.  Reclamation biologists leading this effort have over 15 years' experience as fisheries biologist working with a variety of salmonids and other fishes throughout the western United States.  These monitoring activities had been previously covered and completed under ESA Section 10 research permit (#16608).  Please refer to 2012-2014 Steelhead Monitoring Reports for more detail on equipment and resources that will be used.

Although not anticipated under the proposed action, non-intentional mortality of steelhead due to project activities, should it occur, will be preserved as voucher specimens or sampled for tissue collection, to be sent to the California Department of Fish and Wildlife Central Valley Salmonid Genetic Repository.  Preservation protocols will be confirmed by California Department of Fish and Wildlife scientist Robert Titus.  Any tissues/mortalities of juvenile steelhead that are unintentionally killed during research activities will be made available to NMFS upon request.

Annual reports of steelhead monitoring activities will be provided to NMFS for posting on their website.  Annual reports will include: a detailed description of activities conducted, electrofishing data, description of any unforeseen problems or effects, description of effects on animals, method used to estimate take if different from proposed method, steps taken to coordinate actions with other permit holders, summary of project findings, and titles of reports available.