Author Archives: Tom Cannon

Obsession with Fall X2

Posted on by

There is a science-management obsession with Fall X2 – the location of the 2 parts-per-thousand salinity location in the Bay-Delta in the autumn.  More specifically, Fall X2 is the average km location of X2 for the months of September-December.  Such an average index seems ridiculous given that X2 varies so much especially in December, or even in a year like 2016 in October-November.  Despite this, resource agencies have been intent on trying to manage the Delta smelt population by manipulating Fall X2 based on the relationship between Fall X2 and the following spring 20-mm survey smelt index shown in Figure 1.  Fall X2 is an element of Action 4 in the Smelt OCAP Biological Opinion.

Figure 1. Fall X2 versus 20-mm Survey Delta smelt index.

Figure 1. Fall X2 versus 20-mm Survey Delta smelt index.

The problem is not that fall flows and X2 location are not important to Delta smelt. It’s that the previous year’s winter-through-fall flows, Delta exports, and fall adult population abundance are all related to the subsequent year’s production of smelt. So are winter-spring conditions. Smelt production in any year is related to all these factors, with some factors being more important in some years. A spring index can be low for many reasons, including bad conditions that spring regardless of the location of X2 the previous fall.

Focusing on any one parameter like Fall X2 is dangerous. Since there is only limited water in a drought year, it is critical that available water be distributed in a way it does the most good. If all the smelt die in June, it doesn’t help much to allocate a lot of water in the fall.

Figure 2. River kilometer reference locations for X2. Collinsville (km 81), Mallard Island, and Port Chicago are standard reference locations when specifying X2 standards.

Figure 2. River kilometer reference locations for X2. Collinsville (km 81), Mallard Island, and Port Chicago are standard reference locations when specifying X2 standards.

The Fall X2 factor is being studied in the FLaSH program.1 The study is being undertaken as an adaptive management experiment. “According to the FLaSH conceptual model, conditions are supposed to be favorable for Delta Smelt when fall X2 is approximately 74 km or less, unfavorable when X2 is approximately 85 km or greater, and intermediate in between (Reclamation 2011, 2012). Surface area for the LSZ at X2s of 74 km and 85 km were predicted to be 4000 and 9000 hectares, respectively (Reclamation 2011, 2012).”

The Smelt BO is being revised by the US Fish and Wildlife Service. The State Board is considering new Delta water quality standards for the Delta. Let’s hope they place less emphasis on the Fall X2 factor and more emphasis on progressively managing hydrology, water quality, and fish populations in the Bay-Delta.

Winter-Run Salmon Emigration and First Fall-Winter Rains

Posted on by

In a recent post I discussed the importance of the first fall rains in stimulating the emigration of juvenile winter-run Chinook salmon from the Redding/RedBluff spawning and rearing area of the Sacramento River below Shasta Dam.

Juvenile salmon trap and seine data from fall and early winter of 2015 and 2016 further support the importance of these first-of-season rains to the emigration of winter-run salmon emigration to the Delta, Bay, and ocean. The pertinent data were obtained from trap and seine collections from four locations (Red Bluff, Tisdale-Wilkins, Knights Landing, and Sacramento) shown in Figure 1.

This year’s (2016) fall migration pattern (Figure 2) shows the marked uptick in movement (catch) with the late October storms. Movement had begun gradually in early September from Red Bluff to Tisdale Weir, with some fish showing up at Sacramento. Most of the fish located above Sacramento seemed to take advantage of the storm-water surge, since the plots for the cumulative capture of juvenile salmon at the Red Bluff, Tisdale Weir, and Knights Landing locations flattened off after the storms.

The previous year’s (2015) migration pattern (Figure 3) indicates that the fish waited until the first storms at the end of fall and beginning of winter before moving from the river into the Delta at Sacramento. The March movements indicated in Sacramento and Chipps Island (entrance to SF Bay) trawl catches are indicative of February-March stocking of hatchery smolts near Redding – these larger smolts are not readily detected in river screw traps and seines.

A recent study report1 describes how low flows result in “long in-river residence and low survival whereas strong peak flows corresponded to rapid emigration and high survival… Overall, this study highlights the importance of pulsed flow conditions for promoting higher survival of juvenile Winter-Run Chinook Salmon emigrating to the ocean.” The study notes that survival is proportional to the cumulative catch. Note that the catch in 2016 is nearly 50% higher so far than it was in 2015.

The recent data confirms the need to bypass some of the inflow to Central Valley rim dams during early storm pulses. This bypass of flow to spawning and rearing areas just downstream of the dams gets salmon moving downstream. It is equally important to limit Delta exports during these peak juvenile emigration periods. Success during storm events is critical for endangered salmon to reach the Bay and ocean.

Figure 1. Location of four trap and seine locations in Sacramento River between Red Bluff (river mile 243) and Sacramento (river-mile 54).

Figure 1. Location of four trap and seine locations in Sacramento River between Red Bluff (river mile 243) and Sacramento (river-mile 54).

Figure 2. Winter-run Chinook salmon cumulative catch at Sacramento River collection sites in fall 2016 plus river flow at Wilkins Slough gage (CDEC data).

Figure 2. Winter-run Chinook salmon cumulative catch at Sacramento River collection sites in fall 2016 (www.cbr.washington.edu/sacramento), plus river flow at Wilkins Slough gage (CDEC data).

Figure 3. Winter-run Chinook salmon cumulative catch at Sacramento River collection sites in fall-winter 2015 (www.cbr.washington.edu/sacramento), plus river flow at Wilkins Slough gage (CDEC data)

Figure 3. Winter-run Chinook salmon cumulative catch at Sacramento River collection sites in fall-winter 2015 (www.cbr.washington.edu/sacramento), plus river flow at Wilkins Slough gage (CDEC data)

  1. http://scienceconf2016.deltacouncil.ca.gov/sites/default/files/2016-11-02-Accepted-Poster-Abstracts.pdf. Emigration Rate and Survival of Winter-run Chinook Salmon. Jason Hassrick, ICF International, jason.hassrick@icfi.com. Arnold Ammann, NOAA Southwest Fisheries Science Center, arnold.ammann@noaa.gov. p. 64. ↩

Issues in Delta Smelt Science

Posted on by

Header Image

Recently the San Francisco Estuary & Watershed Science journal published a special issue that included a paper on Delta Smelt.  The paper is an excellent summary of the present state of Delta smelt.  The discussion section on p. 18 of the paper provides an excellent description of the whole of Delta Smelt science.  The paper is comprehensive with a litany of scientific references on Delta science and the decline of the Bay-Delta estuary and the Delta Smelt.  It also provides an outlook and prescription for the future, though bleak.

In this post I offer slightly more optimism with focused solutions, based on a somewhat different take on several key issues.  Bear with me as I go through each issue and my usual array of diagnoses and recommended treatments that could bring smelt back from the brink.

Population Dynamics – What drives smelt numbers

“The role of density dependence has been an area of emphasis for these population dynamic studies. An apparent decrease in the carrying capacity of the estuary in the 1980s resulted in an increase in density-dependent mortality from the juvenile stage in late summer through the adult stage in fall (i.e., between the TNS and FMWT indices) (Sweetnam and Stevens 1993; Bennett 2005; Maunder and Deriso 2011).” p. 9.

Density-dependent mortality means that fish get so abundant that it reduces their growth and survival through competition.  There is no evidence of this dynamic in the Delta smelt population indices (Figure 1).  The number of smelt in fall is simply related to summer flow and exports, and most importantly to the starting number of summer juveniles, which is most certainly related to flow and exports (Figure 2).  The latter is density independent – survival was not lower at higher initial numbers or vice versa.  Density dependence might be expected in conditions of very, very high abundance of juveniles that competed amongst each other for food, possibly even driving down their food supply.  That is simply not possible at the extremely low population levels that exist at present and that have existed in the recent past.

“In general, the relationship between sub-adult (spawner) abundance indices and juvenile abundance in the following year is poor (i.e., between the FMWT and TNS indices).” p. 9.

No, the relationship between spawner abundance and juvenile abundance is strong (Figure 2).  The number of young smelt produced is much reduced in most dry years because of their lower flows and higher exports.  Low exports in the wetter years 2010 and 2011 from restrictions in the 2008 Smelt Biological Opinion really helped.  Those restrictions were not in place in red-circled 2005.

“This suggests that inter-generational abundance is driven more by environmental conditions, rather than by density-dependent factors.” (Id.)  

What they are saying is that the number of young produced each summer is determined by environmental factors, which is true.  But the most important factor remains the number of adult spawners at the beginning of the year, as represented by the fall index.  It is a vicious circle, with environmental factors (flow and exports) driving the population down to the point that production even in good environmental conditions (2010, 2011) is low because of the depressed population (low number of eggs produced).  This defining problem is important, because under the paper’s conclusion, the population can come back under good conditions. That is not possible with the stock size low.  The authors seem to recognize this:

“Given the annual life cycle, any episodic salvage event may undermine population resilience by keeping numbers low, even when environmental conditions are good.” (p. 14).

Figure 1. Strong Stock Recruitment relationship. Summer to fall abundance plotted using log of numbers. Summer Townet (STN) Index in June. Fall Midwater Trawl (FMWT) Index in Sep-Dec. Lower survival in high export/low outflow dry summers like 77, 78, 81, 94, 02, and 04. Lower survival in flood years 82, 83, 86, 96. Higher survival in low export summers 90-92 when they ran out of water for export, and 72 when Andrus Island levee broke. (Source: http://calsport.org/fisheriesblog/?p=810 )

Figure 1. Strong Stock Recruitment relationship. Summer to fall abundance plotted using log of numbers. Summer Townet (STN) Index in June. Fall Midwater Trawl (FMWT) Index in Sep-Dec. Lower survival in high export/low outflow dry summers like 77, 78, 81, 94, 02, and 04. Lower survival in flood years 82, 83, 86, 96. Higher survival in low export summers 90-92 when they ran out of water for export, and 72 when Andrus Island levee broke. (Source: http://calsport.org/fisheriesblog/?p=810 )

Figure 2. Strong Stock Recruitment relationship. Fall to next summer abundance plotted using log of numbers. Summer Townet (STN) Index in June. Fall Midwater Trawl (FMWT) Index in Sep-Dec. Blue years – wet; red years – dry. Year 05 suffered from low number of spawners and high exports. Years 2010 and 2011 (green circles) were wetter with low exports under OMR restrictions – gave us some hope, but operations in following 4 years of drought ended that, as the past several years points have been at bottom left. (Source: http://calsport.org/fisheriesblog/?p=810 )

Figure 2. Strong Stock Recruitment relationship. Fall to next summer abundance plotted using log of numbers. Summer Townet (STN) Index in June. Fall Midwater Trawl (FMWT) Index in Sep-Dec. Blue years – wet; red years – dry. Year 05 suffered from low number of spawners and high exports. Years 2010 and 2011 (green circles) were wetter with low exports under OMR restrictions – gave us some hope, but operations in following 4 years of drought ended that, as the past several years points have been at bottom left. (Source: http://calsport.org/fisheriesblog/?p=810 )

Predation

“Presently, Mississippi silverside is probably the most important predator of Delta Smelt larvae because of their ability to prey on eggs and larvae and their high abundance in shallow areas where Delta Smelt spawn (Bennett and Moyle 1996; Bennett 2005; Baerwald et al. 2012).” p. 14.

“Although Delta Smelt remained abundant in the Delta and Suisun Bay through the 1970s, long after most introduced fish predators and competitors had established populations (Grossman, this volume), smelt began rapidly declining after the invasions of overbite clam and Mississippi Silverside in the 1980s.” p.7.  

Silversides were also abundant in the late 70’s (no 80’s invasion), but were in my opinion suppressed by very abundant juvenile striped bass.  This effect persisted until the striped bass population crashed at the beginning of the new century.  Note the relative abundance of silversides (smelt predator and competitor), threadfin shad (competitor), and yellowfin goby (predator and competitor) in the western Delta in 2006 (Figure 3), and the low density of striped bass.  Next, note the depressed relative abundance of these same species in the western Delta in late summer and fall of 1978 (Figures 4-7).  Note also the much greater abundance of juvenile striped bass and even some Delta smelt in 1978.  While such evidence may be circumstantial, it clearly shows the role that striped bass once played as the dominant predator in the Delta.  Now I have to ask the questions: (1) what caused the “invasion” of silversides in the 80s; and, (2) what was the role of striped bass?

“Largemouth Bass will consume Delta Smelt in mesocosms (Ferrari et al. 2014), but are unlikely to be a major predator in the wild because of limited habitat overlap between the two species.” p. 15.

There really is no proof of this.  Largemouth are found pretty much throughout the Delta, including areas where juvenile smelt are found in summer and fall.  With largemouth far more abundant than smelt, it is likely that smelt come across largemouth frequently.  I have caught both species in the same seine in the fall, on several occasions.

Habitat Change – water temperature and salinity

“While Delta Smelt have a fairly broad salinity tolerance; they were historically most abundant in the low salinity zone (LSZ) of the estuary, the position of which is determined by outflow (Moyle et al. 1992; Kimmerer et al. 2013; Sommer and Mejia 2013). Moderate hydrological conditions in late winter and spring place the LSZ in the Grizzly Bay region of Suisun Bay (Jassby et al. 1995). These conditions were beneficial to the Delta Smelt population at least partly because of high food abundance. At present, there is little evidence of the benefit of summer and fall occupancy in the LSZ (IEP MAST 2015).” p. 16.

Occupancy of the low salinity zone is a benefit to smelt in those wetter years when the water temperatures in the LSZ are not lethal to smelt. The LSZ (roughly 0.5 to 6 ppt salt) and its internal focal point X2 (2 ppt) are indeed critical to the  summer-fall success of smelt in the Delta.  Food is generally more abundant and water temperature is generally lower in the LSZ than in fresher upstream waters. Lower temperature and slightly brackish water allow lower energy consumption (smelt blood serum is approximately 2 ppt).  Smelt are adapted to X2, prefer X2, and are found primarily at X2.  X2 and the LSZ are a major ecological theme for many estuarine species around the world.  In 2014 and 2015, X2 was located too far upstream in the Delta because the State Water Board weakened Delta water quality requirements, resulting in lethal water temperatures for smelt in summer and fall.  The smelt had no place to go.  X2 belongs further west under the protection of the “Delta Breeze” and away from the influence of the South Delta export pumps.  It really is that simple.  [Note: on July 15, 2016, the State and Federal water projects bumped up Delta outflow from 7,000 cfs to 14,000 cfs by reducing exports while holding inflow (reservoir releases) constant in an effort to meet Delta salinity standards, pushing the few remaining smelt and X2 west of the Delta.  Was this action beneficial to Delta smelt? We will have to see.]

“Warm water temperatures during summer exacerbate stress from low food availability and may explain reduced survival from summer to fall in some years (Bennett 2005; Bennett et al. 2008).” p. 14.

“In addition to moving the LSZ to a favorable location for smelt, increased outflow influences habitat quality through its effect on food supply, dilution of contaminants, and turbidity.” p. 16.

Water temperatures are a problem in most summers, especially when the LSZ is located in the Delta.

Hatchery

“Reintroductions will have to be done within a few years of loss of wild fish, into an environment with better capacity to sustain them.” p. 19.

The X2 location in fall offers good habitat in most years.  The problem is that juveniles are unable to survive to get to LSZ.  The carrying capacity of the LSZ in the fall is likely underutilized in most years.  Adding hatchery fish now to surviving wild fish will be better than waiting for wild fish to be gone.  It might be essential at this point.

Refuges

“If increasingly unfavorable temperatures for smelt occur, predicted as a result of climate change, then special refuges may have to be created that can take advantage of cooler water in  the Sacramento River or from water that is piped in from some other source.” p. 20.

Existing refuges already need protection.  The Ship Channel and lower Cache Slough refuges can take advantage of the cooler water exiting the American River near the Port of Sacramento River.  Flow from the Fremont or Sacramento weirs could enhance Yolo Bypass flows and water temperatures.  The LSZ-X2 refuge can be cooler if located west of the Delta and subject to the Bay breeze; maintaining x2 west of the Delta would require higher spring, summer and fall Delta outflow.  Protection and enhancement of the Montezuma Slough refuge portion of the LSZ is possible through better Delta outflows and controls offered by the Montezuma Slough Weir.

Summary of Potential Recovery Actions

The following actions, if implemented soon, could lead to marked improvement in the population of Delta smelt.

  1. Limit entrainment. Minimize exports in spring, especially when pelagic larvae are found in the central Delta.
  1. Keep the LSZ out of the Delta, especially in warm, dry years. Use the Montezuma Salinity Control Weir to maintain Montezuma Slough in Suisun Marsh as part of the LSZ.
  1. Enhance the spring Delta inflows from the Yolo Bypass and San Joaquin River. Opening the Delta Cross Channel and installing the Head-of-Old-River and False River barriers will help.  Closing the Knights Landing Outfall Gates in dry years will force more flow down the Yolo Bypass.  Constructing the “Notch” in the Fremont Weir will increase flow through the Yolo Bypass.  “Fixing” the entrance gate at the Port of Sacramento to the Ship Channel would allow additional Sacramento River flow input to the Ship Channel and lower Bypass.
  1. Stock hatchery-reared Delta smelt adults in the fall at X2 location, conditions permitting.
Figure 3. Numbers of fish collected in the fall of 2006 along San Joaquin River shoreline near Antioch by species and size. Note the extreme abundance of silversides, followed by threadfin shad and yellowfin goby. Note the very low numbers of striped bass.

Figure 3. Numbers of fish collected in the fall of 2006 along San Joaquin River shoreline near Antioch by species and size. Note the extreme abundance of silversides, followed by threadfin shad and yellowfin goby. Note the very low numbers of striped bass.

Figure 4. Numbers of fish collected in late summer 1978 along San Joaquin River shoreline near Antioch by species and size. Note the relatively high numbers of striped bass relative to silversides and threadfin shad.

Figure 4. Numbers of fish collected in late summer 1978 along San Joaquin River shoreline near Antioch by species and size. Note the relatively high numbers of striped bass relative to silversides and threadfin shad.

Figure 5. Numbers of fish collected in late summer 1978 in Sacramento River shoreline near Montezuma Island (adjacent to Collinsville) by species and size. Note the high relative abundance of striped bass young. Delta smelt were actually more abundant than silversides, yellowfin goby, or threadfin shad.

Figure 5. Numbers of fish collected in late summer 1978 in Sacramento River shoreline near Montezuma Island (adjacent to Collinsville) by species and size. Note the high relative abundance of striped bass young. Delta smelt were actually more abundant than silversides, yellowfin goby, or threadfin shad.

Figure 6. Numbers of fish collected in fall 1978 in San Joaquin River shoreline near Antioch by species and size. Note silversides were relatively abundant along with striped bass and threadfin shad.

Figure 6. Numbers of fish collected in fall 1978 in San Joaquin River shoreline near Antioch by species and size. Note silversides were relatively abundant along with striped bass and threadfin shad.

Figure 7. Numbers of fish collected in fall 1978 in Sacramento River shoreline near Montezuma by species and size.

Figure 7. Numbers of fish collected in fall 1978 in Sacramento River shoreline near Montezuma by species and size.

Stocked Trout Fisheries

Posted on by

A recent paper in the North American Journal of Fisheries Management1 describes a nationwide 20% decline over the past two decades in sport fishing for trout.  The trout angling population is getting older, while the number of young recruits is declining.  With shrinking revenues from license sales, trout anglers and agencies are concerned about potential reductions in the numbers of trout stocked and the quality of popular trout fisheries supported by stocking.

Though the researchers found little relationship between the numbers of trout stocked and catch rate (within normal levels of stocking and catch rates), they did find a positive relationship between angler satisfaction and catch rate in the Virginia lakes and rivers they studied.  They also found greater satisfaction with greater size of trout caught.  Average catch rates of stocked trout were approximately one per hour.  Total angling hours were much higher for lakes than streams primarily because of ease of access and less need for equipment.

Because numbers of trout stocked were not significantly related to catch or angler satisfaction, the researchers suggested reductions in stocking rates to counteract longterm losses in license revenues.   Because this would seem counter-productive to sustaining angler interest and effort, they suggested:

“Beyond catch metrics, we believe that demystifying the programs by increasing transparency and increasing the communication of stocking densities and the persistence of catch rates—two common concerns—may increase retention and possibly lead to the recruitment of new anglers. We encourage information exchange between agencies and their anglers.”

This past June, I wrote a post on Lake Davis, a popular Sierra trout fishery.  In that post, I spoke of perceived angler dissatisfaction with low catch rates.  Rates had fallen well below one-per-hour in recent years, into the range where angler satisfaction was very low in the above-described research paper.  I suggested that the poor catch rate was possibly due to low stocking rates, although other factors were possible (e.g., drought-related low water levels).  This fall, I have noticed a sharp uptick in the catch rate at Lake Davis and a corresponding increase in angler satisfaction and effort.  Catch rates from both shore and boat, for both bait and fly anglers, increased into the 0.5 to 1 fish per hour range, with the large size of the fish pushing angler satisfaction (and seasonal effort) to near maximum.  Given the large average size of the trout, I assume the catch rate increase is not due to higher stocking rates, because fish are usually relatively small when they are stocked.  A reasonable hypothesis is that warm water in Lake Davis, due to low water levels and lack of snowmelt this past spring and summer, probably put fish off the bite.

A final thought on declining numbers of licensed anglers.  While CDFW does sponsor activities that promote angling for young people (see photo below), there is no general program promoting efforts, projects, and specific fisheries around the state.  A more comprehensive program designed to increase angling participation, such as the programs offered by other states (e.g. Michigan, Oregon, Texas, etc.), would help to increase angler recruitment.  I like Michigan’s weekly fishing report and its fishing tips reports.  CDFW needs to generate more excitement with up-to-date news, tips, maps, and techniques.  Biologists, wardens, and creel census clerks collect a lot of information that they could share through volunteers or the CDFW blog.  CDFW could also post, link or summarize reports from guides and shops (while giving appropriate credits).  CDFW could also report on how it is managing fisheries around the state how these fisheries are faring.  One topic of interest to many anglers I know is a new fishery that has appeared in the American River, apparently as a consequence of stocking trout (steelhead smolts) from the Battle Creek hatchery (Redding) in the American River (see photos below).

Fishing in the City event sponsored by CDFW. Young people love these events, but the program needs to follow up with other elements to sustain their interest.

Fishing in the City event sponsored by CDFW. Young people love these events, but the program needs to follow up with other elements to sustain their interest.

Are these American River fish steelhead from the Battle Creek Hatchery?

Are these American River fish steelhead from the Battle Creek Hatchery?

Water Year 2016

Posted on by

At an October 27, 2016 meeting of the Delta Stewardship Council, John Leahigh, Department of Water Resources chief operator for the State Water Project, briefed the council on Water Year 2016. Precipitation-runoff and reservoir storage were up considerable compared to 2014 and 2015.  However exports were lower than expected, with reduced deliveries – only 5 to 75% – to south of Delta water contractors.

water-year-2016Mr. Leahigh attributed lower Delta exports to several factors:

  • A concerted effort to conserve Shasta storage (for winter-run salmon) at the expense of water deliveries, mainly to south-of-Delta contractors.
  • Higher summer Delta outflow that was needed to repel saltwater intrusion into the Delta caused by higher-than-normal tides associated with the warm-water “blob” along the coast. (This outflow served the dual purpose of reducing the salinity of Delta export water and allowing the water projects to meet salinity standards for Delta agriculture – see previous post.)
  • Lower San Joaquin River Delta inflow that “creates a dynamic in the Delta that makes it difficult to move stored water from the Sacramento basin to the south Delta”.
  • An inability to export Valley stormwater in winter-spring: “If we don’t pick it up, it ends up in the Bay and into the ocean.”  (This is a not-too-subtle reference to winter-spring export restrictions for endangered fish and pitch for the proposed Delta tunnels.)

Mr. Leahigh concluded:  “I think the key messages would be flexibility, nimbleness, and the fact that we have processes in place that would help us react to whatever we end up seeing in the coming year; there’s always a new challenge with respect to the hydrologic pattern and the regulatory environment, so just having those processes in place puts us one step forward.”

The important lesson here is that the state and federal water projects are flexible and nimble when it comes to water exports and deliveries.  When it comes to the short-term needs of the fish and their habitat, not so much.  The projects are ready with Temporary Urgent Change Petitions to benefit water deliveries, but not the environment.