Category Archives: Bay-Delta

Enhancing Coleman Hatchery Salmon Contribution

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In a recent post I discussed ways to improve hatchery salmon smolt survival to increase coastal and river salmon populations devastated by recent droughts. This post is a follow-up addressing how to enhance the Coleman (Battle Creek) Hatchery1 contribution. Coleman produces nearly half of the Central Valley’s 30 million hatchery-produced salmon smolts. Three state hatcheries in the Valley (Feather, American, and Mokelumne) produce most of the other smolts. Survival of Coleman hatchery smolts released to the Sacramento River is markedly lower in dry years.2 Trucking smolts from the hatchery to the Bay increases survival and catch in fisheries, but at a cost of increased straying and low return rates of adults to the hatchery.

Of all these hatcheries, Coleman has the toughest challenge, because it is nearly 300 miles from the Golden Gate. While trucking smolts to the San Francisco Bay improves smolt survival and adult salmon population numbers available to fisheries, trucking from Coleman leads to low hatchery-return rates and excessive straying to other Valley rivers. Only about 50-100 adults per million smolts trucked to the Bay find their back to Coleman. In contrast, for each million smolts released at the hatchery, 400-500 return to Coleman to contribute eggs for the next generation.

One measure to increase smolt survival-contribution I suggested in past posts is barging smolts to the Golden Gate. Unlike trucking, barging allows some imprinting by smolts for their eventual return route back to the hatchery. Barging requires a medium to large sized vessel, which would still necessitate nearly 200 miles of trucking to barge-accessible locations on the lower Sacramento River. Barging may reduce straying while providing enhanced smolt survival to the Bay, although past trucking and release at Knights Landing in the lower river only marginally lowered the straying rate compared to Bay releases. A balance between overall survival and contribution to the fishery and returns to the hatchery is the challenge for fisheries managers. Barging from Knights Landing or Elkhorn boat ramps may provide more returns to the Sacramento River above the mouths of the Feather and American rivers than trucking releases to these locations or the Bay. Regardless, barging should provide substantially higher survival and returns to the upper river than river release of fish, especially in dry years. Barging test studies conducted by the Feather Hatchery program should be expanded to test potential benefits of Coleman salmon smolt barging.

Another measure that deserves testing is rearing Coleman fall-run fry off-site in Yolo Bypass rice fields. The higher survival and growth potential and earlier ocean entry of these smolts compared with smolts released at the hatchery, should increase the numbers of adult salmon available to the fisheries. Concerns include low returns to Coleman hatchery and straying of returning adults back to the Yolo Bypass. The State’s EcoRestore Program is planning fish passage improvement projects in the upper Bypass. Barging off-site-reared smolts to the Bay from nearby Knights Landing or Elkhorn boat ramp could potentially improve return rates to the hatchery and overall survival, especially in dry years

A third proven measure that is possibly more promising and readily implementable is improving downstream migration conditions for smolts released to the upper Sacramento River from the Coleman hatchery. Smolt survival and contribution to fisheries and adult returns to the hatchery are better when flow, turbidity, and water temperature conditions are good at the time of release and in the immediate weeks thereafter in the 200 miles downstream to the Bay. To a certain extent, the hatchery can time releases to river conditions (and does so when feasible). However, the timing of smolting and the whole rearing process necessitates a week 15-17 release window (late April to beginning of May). When conditions are optimal in these key weeks, survival and contribution rates of smolts released at Coleman are nearly as high as they are for smolts transported to the Bay. Such 1-3% survival (returns) would produce hundreds of thousands of adults, compared to just tens of thousands under poor conditions when there is just 0.2-0.5% survival (Table 1). A 3% survival would yield 360,000 adult salmon returns from 12 million hatchery smolts, as compared to only 12,000 returns under a 0.1% survival.

So what are good conditions in late April? Adequate stream flows are those necessary to meet existing water quality standards, water right permits requirements, and endangered species permit requirements in the upper 200 miles of river below Shasta Dam. Such prescriptions are basically minimum targets: keeping the upper river within the 56oF limit upstream of Red Bluff and the river downstream to the Delta at 68oF or less. These standards were put in place decades ago to protect beneficial uses, including salmon survival.

The problem is that these standards are both increasingly being ignored and violated, and are also proving inadequate in providing optimal smolt survival. Figure 1 shows that standards were violated at Red Bluff, even in 2017, a record water supply year. Figure 2 shows 2017 water temperatures at Wilkins Slough in the lower Sacramento River. Though water temperatures remained below 68oF (20oC) during the period shown, they reached above the 65oF (18oC) stress level for migrating juvenile salmon. Such high water temperatures place the smolts at much greater risk to predation.3 Even in this record water supply year, water was unnecessarily held in storage in Shasta Reservoir at the expense of Coleman and wild salmon smolt survival. When water contractor demands are low and Delta conditions are “in excess,” there is a tendency in all year types to maintain Shasta storage at the expense of lower river water temperature and Coleman smolt survival.

In addition to maintaining flows and water temperatures, a flow pulse through the lower river in the late April to early May period would likely improve survival. A flow pulse in drier years would provide higher transport rates, higher turbidity, and lower water temperatures, conditions that often occur in wetter, high survival years. A one week pulse that raised flows from the “dry” year 5000 cfs flow level to a 10,000 cfs level would use approximately 10,000 acre-ft per day, or about 70,000 acre-ft for a week. At Shasta Reservoir’s current storage level in excess of 4 million acre-ft, the water needed for a one week flow pulse would be less than 2% of the total storage for the year. Even for a multiyear drought year like 2015, the amount needed would be only 3 to 4% of total annual storage. While drought year pulses would need to be weighed against losses to the Shasta coldwater pool, a 1% improvement in dry-year survival would add 120,000 adult salmon from the 12 million smolts produced by the Colman hatchery. For a dry year or drought year sequence, the increase could be over 100% over current survival rates, and could allow a salmon fishing season when there might otherwise be none.

In summary, the salmon fishery collapses that occurred as a consequence of the 2007-2009 and 2012-2015 droughts could have been at least partially alleviated by improving survival of smolts produced at the Coleman hatchery. Compliance with spring water temperature standards in the lower Sacramento River would help greatly. When water supplies are adequate, spring flow pulses should be considered. Barging Coleman smolts to the Bay and off-site rearing in lower river floodplain habitats are additional measures to test in order to increase Coleman hatchery smolt survival and contributions to ocean and river fisheries.

Table 1. Survival (return) rates of Coleman hatchery fall run Chinook salmon release groups for a range of year types.
Source of survival data: http://www.rmpc.org.

Water Year Week 15-17 Conditions Smolt Survival4
1997 Wet Year Lower River conditions were deteriorating in April with flows falling from 7000 to 5000 cfs and water temperatures rising from 59oF (15oC) to 65oF (18oC). Week 15 – 0.8%
Week 16 – 0.3%
Week 17 – 0.2%
1998 Wet Year Lower River conditions were near optimal with 18,000 cfs flow and water temperature of 15oC. Week 17 – 0.9%
2002 Dry Year Lower River conditions degraded gradually from week 15 to week 17).  Flows in lower river fell from near 10,000 cfs to less than 5000 cfs during April.  Though water temperatures remained below 68oF (20 o C) during the period, they often reached above the 65oF (18 oC) stressful level for migrating juvenile salmon. Week 16 – 0.8%
Week 17 – 0.6%
2007 Critical Dry Year Lower River conditions were poor in weeks 16-17 with flows of 4000-5000 cfs and water temperatures of 19-21oC. Week 16 – 0.01%5
2008 Critical Dry Year Lower River conditions were poor with flows of 5000 cfs and water temperatures 16oC to 18oC in weeks 16-17, but reaching 20-22oC in week 18. Week 16 – 0.1%
Week 17 – 0.1%
2009 Critical Dry Year Lower River flow decreased from 7000 cfs to 5000 cfs in weeks 15-16, while water temperature rose from 15oC to 20oC.  Flow pulsed to 10,000 cfs in week 17 dropping water temperature to 15oC. Week 15 – 0.5%
Week 16 – 0.9%
2011 Wet Year Lower river flows in April were dropping sharply from 16,000 to 8,000 cfs, with water temperature rising from 15oC to 18oC. Week 15 – 2.2%
Week 16 – 1.5%
Week 17 – 1.2%

Figure 1. May 2017 flow and water temperature conditions in upper Sacramento River. Source: CDEC.

Figure 2. May 2017 water temperature in lower Sacramento River at Wilkins Slough. Source: CDEC.

  1. The Coleman Hatchery near Redding on Battle Creek is operated by the US Fish and Wildlife Service. The hatchery operates under the Central Valley Project as mitigation for Shasta Dam on the upper Sacramento River ↩
  2. http://calsport.org/fisheriesblog/?p=1703 ↩
  3. http://calsport.org/fisheriesblog/?p=878 ↩
  4. Survival rate is defined as percent of smolts that were subsequently collected as adults in fisheries, spawning surveys, and at Central Valley hatcheries. Average rate of multiple groups is shown. ↩
  5. Poor ocean conditions in 2007-2009 likely contributed to poor survival. ↩

Splittail Status end-of-June 2017

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Last time I posted on splittail, it appeared that the species remained relatively abundant (though declining) in its core population centers in the Bay. I was concerned about population recruitment during the 2012-2015 drought and whether there were sufficient adults remaining to bring about a strong brood year in wet year 2017. The traditional summer and fall surveys will be the best indicator of success. At the end of spring, the best interim indicator is splittail salvage at south Delta SWP and CVP export facilities. In wet years, south Delta export salvage likely best reflects San Joaquin River splittail production.

I compare salvage in 2011 with 2017 in Figures 1 and 2 for the SWP and CVP, respectively. These were the only wet years since 2006. Wet years provide good spawning and rearing conditions for splittail. These conditions often create strong year classes of juvenile and adult splittail as shown in summer and fall fish surveys in the Delta and the Bay.

Though the density of juvenile splittail in salvage is lower in 2017 than 2011, winter and early spring flows were higher in 2017, which could have led to broader dispersal. Very high late winter and early spring flows in the lower Sacramento River system including the Yolo Bypass may have transported north-of-Delta splittail production directly to the Bay, bypassing the south Delta and its export facilities. Spring flows in the two years were similar in magnitude when young splittail traditionally move downstream through the Delta toward the Bay. It remains to be seen whether the difference in salvage plays out as a discrepancy in recruitment in the Bay populations. Local spawning recruitment in the Napa and Petaluma rivers and in Suisun Bay/Marsh could be strong in years like 2017 and could make up for lower recruitment from the Sacramento and San Joaquin river valleys. The primary concern is long term trends in the core adult population centers in the Bay that for now remain strong.

Splittail Salvage at SWP Byron Facility

Figure 1. Splittail salvage density (number per 10,000 cubic meters exported) at State Water Project Delta export facility in May and June 2011 and 2017.

Splittail Salvage at CVP Tracy Facility

Figure 2. Splittail salvage density (number per 10,000 cubic meters exported) at Central Valley Project Delta export facility in May and June 2011 and 2017.

Delta Status End of June 2017

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Despite the fact that it is a record wet year with abundant spring snowmelt, early summer conditions in the Delta in 2017 are not looking good.  Rapidly falling Delta inflows and a late June heat wave have led to salt water intrusion and extremely warm water temperatures detrimental to salmon and smelt throughout the Delta.

Notably, lower Sacramento River flows at Wilkins Slough upstream of the mouth of the Feather River are down about a third compared to the last Wet year, 2011 (Figure 1).  Flow is only about 7000 cfs and water temperatures are 73-75°F, well above the water quality standard of 68°F.  Winter-run and spring-run adult salmon will not move up the river at these temperatures.  Why is flow so low?  Good question.  Shasta is nearly full but releases are down about a third for a wet year at 8000 cfs.  In contrast, the San Joaquin River flow coming into the Delta near Stockton is 13,000-15,000 cfs, with water temperatures of 71-73°F.

Feather River flow contributions to the Sacramento River are very low (Figure 2).  Yuba and American River flow contributions remain strong at about 4000 cfs each.

Overall Delta outflow in late spring 2017 is lower than Wet year 2011 (Figure 3).  Delta inflow is approximately 34,000 cfs, with about equal contribution from the Sacramento and San Joaquin rivers. Delta exports have been maximum through June at 11,400 cfs.  With in-Delta use taken into account, Delta outflow is estimated at 19,000-21,000 cfs. (Note: USGS measured outflow about 14,000 cfs with tides taken into account on June 22.)

With sharply falling Delta inflow and outflow, high exports, and the heat wave, the Delta is unusually warm at 72-75°F. Such temperatures are detrimental to juvenile smelt, salmon, and sturgeon survival.  Juvenile salmon have been present in the Delta well into June on their seaward migrations (Figure 4).

 With falling Delta inflow and high exports, the Delta is stagnating and salt water is intruding at the west end at Chipps Island (Figure 5).  The Low Salinity Zone with the few Longfin and Delta smelt that are left is moving into the Delta on incoming tides.  The water temperature at the head of the LSZ is already 72°F (Figure 6).  Higher temperatures would be very detrimental to surviving smelt and seaward-moving juvenile salmon.  The further east the LSZ moves, the warmer it usually becomes.

There is a consistent late spring pattern in the operation of State Water Project and Central Valley Water Project in which they cut reservoir releases while exporting the remnant freshwater pool in the Delta.  Even in this very wet year we are again witnessing this water supply control strategy.  The problem is the rivers get too warm even to the point of violating water quality standards.  With less water and warmer water entering the Delta, the Delta also becomes too warm.  Delta water quality standards and endangered species permits are supposed to keep this from happening.  Come July 1, conditions will only get worse, especially as snowmelt declines and San Joaquin flows drop sharply.

What can be done?  Both Shasta and Oroville reservoir releases are lower than normal.  Just keeping their cold-water releases near normal and allowing the flows to pass through the Delta would nearly fix the problem.  Exports in the 1970’s and 1980’s were limited to 6000-9000 cfs in June-July of Wet years.  Reducing the present export level of 11,000 cfs would also help.  These would be very reasonable actions given present water supplies in the Central Valley.

Figure 1. Flow in the lower Sacramento River at Wilkins Slough in late spring of 2011 and 2017.

Figure 2. Lower Feather River flow at Gridley upstream of the mouth of the Yuba River.

Figure 3. Delta outflow in late spring 2011 and 2017.

 

Figure 4. Salmon salvage at Delta fish facilities in June 2017. Source: https://www.wildlife.ca.gov/Conservation/Delta/Salvage-Monitoring

Figure 5. Salinity (EC) at Mallard Island gage near Chipps Island (eastern end of Suisun Bay) in June 2017.

Figure 6. Water temperature at Mallard Island gage near Chipps Island (eastern end of Suisun Bay) in June 2017.

How do we increase salmon runs in 2017?

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Over the past few months, I have written posts on the status of specific runs of salmon in rivers throughout the Central Valley.  In this post, I describe the overall status of salmon runs and  recommend general actions to take to increase runs as well as commercial and sport fishery harvests.  The subject is timely given a poor prognosis for the 2017 salmon runs.

It was just a little more than a decade ago at the beginning of the century that there were nearly one million adult salmon ascending the rivers of the Central Valley (Figure 1).  At the same time, there were a million more Central Valley salmon being harvested each year in sport and commercial fisheries along the coast and in the rivers of the Central Valley.  Improvements in salmon management in the decade of the 1990s by the Central Valley Project Improvement Act, CALFED, and other programs had paid off handsomely with strong runs from 1999 to 2005.  New and upgraded hatcheries, combined with the implementation of  trucking hatchery smolts to the Bay, significantly increased both harvest and escapement to spawning rivers.

Figure 1. Central Valley salmon runs from 1975 to 2016 including fall, late fall, winter, and spring runs. Source of data: CDFW GrandTab.

By 2008-2009 escapement had fallen by over 90% to a mere 70,000 spawners of the four major Central Valley runs of salmon.  DFW and the Pacific Fishery Management Council greatly restricted fishery harvest of salmon beginning in 2008.  The winter run, the most threatened of the four runs, fell from 17,296 to 827 spawners in just five years.  Drier years from 2001-2005, poor ocean conditions in 2004-2005, record-high Delta water diversions, and the 2007-2009 drought were contributing factors in these declines.  Impacts to coastal communities and the fishing industries were severe.

Extraordinary recovery measures included closing fisheries and trucking most of the hatchery smolt production to the Bay or Delta.  Federal salmon biological opinions (2009, 2011) limited winter and spring water-project exports from the Delta.  The state and federal governments and others spent hundreds of millions of new dollars on habitat and fish passage improvements in the Valley to improve salmon survival and turn around the declines.  Figure 1 demonstrates that these efforts were somewhat effective in limiting run declines during the 2012-2015 drought, compared to the 1987-1992 and 2007-2009 droughts.

However, the prognosis for 2017 is again bleak.  The consequences of the 2012-2015 drought are about to fully play out.  Once again, projected runs are low and responsible fishery agencies are restricting harvest.  Managers once again must take action to minimize the long term effects and help bring about recovery.

Immediate actions in wet year 2017:

  1. Reduce harvest: Sadly but necessarily, the Pacific Fishery Management Council and west coast states took this first step: they severally restricted the 2017 harvest in the ocean and rivers.
  2. Improve spawning, rearing, and migrating conditions: Sadly, responsible agencies unnecessarily compromised on Sacramento River water temperatures in the first ten days of May, 2017 (Figure 2).  The Bureau of Reclamation released flows as low as 5000 cfs from an effectively full Shasta Reservoir, and water temperature at Red Bluff exceeded the 56oF temperature standards in the biological opinion for salmon and in the Basin Plan.  The resulting high water temperatures affect salmon egg incubation, rearing, and emigration-immigration success.  In one of the wettest years on record, there is no excuse for failure to meet flow and temperature targets in all Central Valley rivers and the Delta.
  3. Limit Delta exports: Delta exports this spring reached unprecedented highs not seen in recent decades, resulting in high salmon salvage rates at the Delta fish facilities (Figure 3).1  With high water supplies in this wet year, there is no need for high exports, especially if it reduces survival of salmon and other native fishes.  If anything, exports should be minimal.

Near-term actions over the coming year:

  1. Transport hatchery smolts to Bay: the transport of millions of fall-run smolts from state hatcheries on the Feather, American, and Mokelumne rivers to the Bay provides higher rates of fishery and escapement contributions and low rates of straying.  Barge transport to the Bay offers potentially lower rates of predation and straying for Federal hatcheries near Redding.
  2. Raise hatchery fry in natural habitats: recent research indicates that rearing hatchery fry in more natural habitat conditions increases growth rates, survival, and contributions to fisheries and escapement.  Raising hatchery fry in rice fields is one potential approach.
  3. Restore habitats damaged by recent record high flows in salmon spawning and rearing reaches of the Central Valley rivers and floodplains: in nearly every river, flooding in 2017 has damaged habitats.  These habitats now  require extra-ordinary repairs and maintenance to ready them again to produce salmon.
  4. With an abundant water supply this year, take further actions to enhance flows and water temperatures to enhance salmon survival throughout the Central Valley: actions may include higher base flows, flow pulses, or simply meeting existing target flow and temperature goals.

In conclusion, managers should take immediate actions to minimize the damage to salmon runs from the recent drought using this year’s abundant water supply.  They should avoid efforts to exploit the abundant water for small benefits to water supply at the expense of salmon recovery and should make every effort to use the abundant water for salmon recovery.

Figure 2. Upper Sacramento River flows and water temperatures in May 2017. The target water temperature for Red Bluff is 56oF. Source of data: USBR.

Figure 3. Export rate and young salmon salvage at South Delta federal and state export facilities in May 2017. The target export rate limit for May is 1500 cfs. Source of data: USBR.

Spring 2017 Delta Fish Salvage

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Though it is counter-intuitive in a flood year, fish salvage has become a real problem this spring.

Total Delta exports reached 8,000 cfs in the first week in May, and salvage of salmon and splittail increased sharply (Figures 1 and 2). Normally, Delta standards limit export limits to1500 cfs in April-May in order to protect fish. However, higher exports are allowed when San Joaquin River inflows to the Delta are high. Even higher exports than the present 8,000 cfs are allowed, but the infrastructure cannot accommodate further exports in this wet year (demands are low and reservoirs south of the Delta are nearly full).

Figure 1. Salvage of Chinook salmon at south Delta pumping plants in spring 2017. Source: CDFW.

Figure 2. Salvage of splittail at south Delta pumping plants in spring 2017. Source: CDFW.

In past wet years, there were restrictions on south Delta exports in April and May to protect juvenile salmon, steelhead, splittail, and smelt that were rearing or passing through the Delta.  These restrictions also protected adult and juvenile sturgeon.  Figure 3 shows an example of Chinook salmon salvage in 1999.  The initial peak in February 1999 salvage was salvage of fry (1-2 inches).  The spring peaks were hatchery and river-reared smolts, primarily from San Joaquin River tributaries.  Both exports and salvage dropped after April 15.

In 2017, with the diversion of over half the San Joaquin River’s flow into the south Delta through the Head of Old River and other channels (Figure 4), there is a definite risk that high export levels will draw young salmon and splittail from the San Joaquin into the south Delta.  Once in the south Delta, they are subject to 8,000 cfs of diversions and a mix of tidal flows.  The risk is even higher than it might seem, because the reported State Water Project diversion is a daily average.  Water enters Clifton Court Forebay for only about one third of the hours in each day, during incoming tides.  The reported 5000 cfs is actually more like 15,000 cfs operating for those eight hours, adding to the pull toward the pumps of the incoming tides.

Reported salvage is just the tip of the iceberg, because predators eat up to 90% of juvenile salmon that enter the Forebay before these juveniles ever reach the salvage facilities.

In conclusion, the State Water Board needs to change the Delta standard.  It needs to limit spring exports even when San Joaquin flows are high.  In 2006 (Figure 5), the now-defunct Vernalis Adaptive Management Program limited April through mid-May exports despite high San Joaquin flows.  Salvage was markedly low during this period of limited exports.

If exports continue high through May and June in 2017, there will be detrimental effects on San Joaquin salmon, steelhead, and splittail, as well as on Delta smelt.

Figure 3. Salvage of Chinook salmon at south Delta pumping plants in winter-spring 1999. Note reduction in exports after mid-April. Source: CDFW.

Figure 4. High tide flows in the Delta at the beginning of May 2017. Blue represents positive downstream flows during high tides, where tides had minimal influence. Red denotes upstream tidal flow during incoming tides.

Figure 5. Salvage of Chinook salmon at south Delta pumping plants in winter-spring 2006. Note reduction in exports in early April. Winter-spring San Joaquin flows in 2006 were similar to those in 2017. Source: CDFW.