Category Archives: Fish (general)

A “Winter-Run Critical Habitat Conundrum”

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Figure 1. Lower American River floodplain referenced in recent science paper as non-natal rearing habitat of endangered winter-run Chinook salmon. Note the many borrow pits from Paradise Beach downstream to Discovery Park, remnants of a historical levee-building era.

Conundrum: A confusing and difficult problem.

The consulting firm FishBio reported in a February 12, 2018 blog post: “Just when you think you’ve got a species figured out, sometimes they show up where they’re “not supposed to be” and make you reconsider. This recently happened in the fish world, when adult winter-run Chinook salmon, an endangered fish previously thought to only inhabit the mainstem Sacramento River downstream of Keswick Dam, were found to have actually reared in multiple Sacramento River tributaries as juveniles.” The study referenced by FishBio found that roughly half of the returning adult winter-run had reared as juveniles for a several weeks or more in habitats other than the mainstem Sacramento River. It has long been known that winter-run had used these habitats1, but the proportion of the population that had done so was not known. The recent study has helped answer that question. Such a life-history pattern is obviously important, as proven by this study.

Juvenile winter-run salmon have frequently been detected in winter in habitats along the Sacramento River from Redding to Rio Vista in habitats where they are not commonly expected to be. In wet years, winter-run are carried into the Butte-Sutter and Yolo bypasses (and other Sacramento River floodplain areas like the lower American River) where they rear as noted in the recent study. I personally have collected large numbers of winter-run juveniles in the 1990’s in Butte Basin, the Bypasses, and the lower American River floodplain (Figure 1). In many cases, floods had carried or backed-up water along with winter-run juveniles into these areas. I have also collected winter-run juveniles (and other juvenile fall/spring salmon) in Suisun Bay, downstream of the Delta. A 2013 report by biologist Michael Healey of the California Department of Fish and Wildlife found that winter-run migrate up Auburn Ravine in Sutter County to rear.2

“These newly identified areas, called “non-natal habitats” because they differ from where the fish was born, can be divided into four distinct groups, including the Mount Lassen tributaries (Mill, Deer, and Battle creeks), the Sacramento-San Joaquin Delta and Feather River, the American River, and a final group rearing in an uncertain location that is not in the Sacramento River.” Again, these are not “newly” identified. Non-natal refers to rearing in adjacent river systems where fish were not born. These habitats are part of the lower Sacramento River floodplain and other accessible habitat of winter-run.

“So even though we might think winter-run are “not supposed to be” using these tributaries, the fish are actually spreading the risk of extinction across multiple habitats to safeguard their future.” These are the natural floodplain and tributary rearing habitats of winter-run. The problem is that there is not enough of these habitats left, and those that are left are often too ephemeral or are in poor condition. In many cases, the young salmon are gain access to floodplains but are later blocked from exiting, only to eventually die and not contribute to the population. Juveniles that enter the lower reaches of tributaries of the Sacramento River are sometimes cut off by seasonal dams or stranded in fields by unscreened irrigation diversions. Often, non-natal habitats (e.g., dredger ponds and borrow pits) are also winter refuges and permanent habitat for predatory warm water fish.

Yes, these non-natal rearing habitats should be recognized, protected, restored, fixed, enhanced, and created where possible to help save the winter-run salmon population. In the meantime, such habitats will continue to support winter-run as they have in the past. There is no “conundrum”.

  1. P.E. Maslin, W.R. McKinney, T.L. Moore. 1996. Intermittent streams as rearing habitat for Sacramento river Chinook salmon. Anadromous Fish Restoration Program, Stockton, CA, United States Fish and Wildlife Service (1996), pp. 1-29 ↩
  2. https://plummerj.files.wordpress.com/2015/01/healey-cdfw-2013-auburn-ravine-rotary-screw-trap-monitoring-report-rs.pdf ↩

Longfin Smelt February 2018

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In April 30, 2017 post on longfin smelt, I wrote that it appeared that longfin were making a comeback after the 2012-2015 drought. In this post I compare the 2017 comeback to those in the two previous wet years, 2006 and 2011.

First: The number of adult longfin smelt collected in the December 2017 trawl survey (Figure 1) was substantially less than the number collected in the December 2011 survey (Figure 2).

Second: The number (density) of larval longfin smelt collected in the late January 2018 larval fish survey (Figure 3) was substantially less than the number collected in the late January 2012 survey (Figure 4).

Third: The 2017 index, though higher than the dry years that immediately preceded 2017 and indicative of some recovery, remained below the recent wet years (06, 11) and continued a long-term trend of progressively lower indices (Figures 5 and 6).

Figure 1. Catch distribution of adult longfin smelt in the December 2017 trawl survey. Source: CDFW survey online report.

Figure 2. Catch distribution of adult longfin smelt in the December 2011 trawl survey. Source: CDFW survey online report.

Figure 3. Catch distribution of larval longfin smelt in the late January 2018 larval fish survey. Source: CDFW survey online report.

Figure 4. Catch distribution of larval longfin smelt in the late January 2012 larval fish survey. Source: CDFW survey online report.

Figure 5. Fall Midwater Trawl Index for Longfin Smelt, 1967-2017. Source: CDFW FMWT Survey.

Figure 6. Longfin Recruits (Fall Midwater Trawl Index) vs Spawners (Index from two years prior) in Log10 scale. Note the progressive decline in recruits in the last three wet years (06, 11, 17). The relationship is very strong and highly statistically significant. Taking into account Delta outflow in winter-spring makes the relationship even stronger. Recruits per spawner are dramatically lower in drier, low-outflow years (red years). Source: http://calsport.org/fisheriesblog/?p=1360 .

Feeding Stripers Again

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Oroville hatchery steelhead smolts being released into the lower Feather River near Boyd’s Pump in early February. CDFW photo.

State and federal agencies have begun stocking over a million steelhead smolts from Central Valley hatcheries into the Sacramento River and its tributaries.1 Fishing reports in the SacBee and other sources note that the annual stocking provokes a strong striper bite in the river, one of the more popular fisheries in the Central Valley.  The yearling smolts are the perfect food for stripers.

Shasta, Oroville, and Folsom reservoir releases are each at about 3000 cfs, low for mid-winter.  As a result, along with the record warm weather, river and Delta water temperatures (Figures 1-4) have been in the preferred range for striped bass feeding (55-65°F).

The federal Coleman hatchery near Redding released its steelhead smolts in January during high flows, before the warm weather arrived and stripers began feeding in earnest.  But at Thermalito Afterbay on the Feather River, the state is stocking a quarter of a million steelhead and feeding bass. And the feds are will be stocking a half-million endangered winter-run salmon hatchery smolts near Redding in February and March.

The striped bass will soon decimate the Feather River steelhead and will be well positioned for the annual April hatchery salmon smolt stocking season in April.  In the meantime, the stripers attracted by massive chumming will be knocking off the wild juvenile salmon and steelhead heading for the ocean.

Why do hatcheries continue to waste so many of the over 20 million salmonid smolts raised each year to mitigate for all the dams on Central Valley rivers?  Smolts cost more than $1 each to raise.

Hatchery managers and their partners need to barge hatchery steelhead and fall-run salmon smolts to the Bay.  Barging smolts would likely increase adult returns sharply in coming years.  Both steelhead and salmon populations are relatively homogeneous genetically, which reduces concerns about the effects of straying.  Coleman smolts should be barged from near Hamilton City.  Oroville smolts should be barged from Verona.  Nimbus smolts should be barged from Discovery Park.

If releases of hatchery smolts into the rivers are to continue, water managers need to at least provide pulsed flows from Shasta Reservoir to help the fish succeed in reaching the Bay and ocean.  Shasta storage is 106% of average.  A 5% allocation to pulsed flows would amount to approximately 140,000 acre-feet, enough for seven days of an 10,000 cfs extra flow to the Sacramento River.  Pulsed flows would also reduce water temperatures.  Hatchery managers should also not  release smolts into the rivers during warm spells that stimulate striper feeding.

State hatcheries plan some trucking of salmon smolts to the Bay-Delta this year, as they have done in past years.  Trucked fish should also be barged or at least taken to the Golden Gate, not just to Rio Vista.

In addition to barging and trucking, and pulsed flows, hatchery managers need to accelerate a pilot program to stock hatchery salmon fry into lower river and Delta floodplain habitats for rearing closer to the Bay.  In these habitats, fry would grow faster than their hatchery counterparts and get to the ocean quicker.

Anglers should take advantage of the great striper fishery.  But let‘s at minimum give the salmonid smolts some chance of reaching the ocean, so we can also once again have great salmon and steelhead fisheries.

 

Figure 1.  Water temperature in early February 2018 in the Sacramento River at the mouth of the Feather River

Figure 2.  Water temperature in early February 2018 in the Sacramento River below the mouth of the American River near Sacramento.

Figure 3.  Water temperature in the lower Sacramento River upstream of the mouth of the Feather River at Wilkins Slough

Figure 4.  Water temperature in the lower Sacramento River in the Delta near Rio Vista.

Hatchery Salmon Are Trained to Be Dysfunctional

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Research has often shown that hatchery salmon perform less well than their wild counterparts.  The reason for this has often been attributed to genetic factors such as parent selection or to the lack of opportunity for Mother Nature to cull misfits.

Recent research indicates that poor performance of hatchery fish may stem more from the their environmental experiences than from their genetics.  Some older theories that suggested that hatchery fish were just raised dumb now have gained a new following.  New research from Canada suggests that atypical food and feeding combined with overcrowding in hatcheries weakens inherent genetic abilities to cope with the natural environment.

In California’s Central Valley, we have added the burden of releasing hatchery smolts late in the natural emigration season outside of peak flow periods, into warmer waters that are full of other fish that want to eat them.  When the salmon from the hatcheries get hungry,  there is no flood of fresh food pellets.  Their new environment results in starvation, thermal stress, and much higher vulnerability to predation.  Still, hatchery fish make up 70-90% of California’s salmon runs, because Valley habitats no longer support historic levels of wild salmon production.

In recent posts, I have advocated raising hatchery fry in Valley floodplain habitats.  UC Davis studies have shown high rates of growth of hatchery fry raised in flooded rice fields during the winter.  New planning efforts call for more flooded Valley habitats, including rice fields, but these efforts focus primarily on wild juvenile salmon.  There has been no testing to date of the performance of hatchery fry that rear under controlled floodplain conditions.  In light of the recent Canadian research, the ability of floodplain-reared hatchery fish to survive, and the degree to which they stray, warrant evaluation.

Measures to Save the Delta and Delta Smelt

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The key to saving the Bay-Delta Estuary and its native fish community is keeping the Low Salinity Zone (LSZ) and its brackish water out of the Delta, especially the south Delta where the federal and state project pumps are located.  The native fish of the estuary, both in the Bay and Delta, depend on potency or productivity of the LSZ.  Much research has shown that low Delta freshwater outflow allows the LSZ to move into the Delta, to the detriment of overall ecological productivity and of the survival and production of native fish (and most pelagic species and their food supply).  Allowing the LSZ to move into the Delta allows the export of the LSZ from the south Delta, to the detriment of native fish and their critical habitats.  Increased salinity also harms agricultural and municipal water supplies.

Keeping the LSZ out of the Delta means keeping salinity (as measured by electrical conductivity or EC) below 500 EC.  The 500 EC level is sometimes called the “salt front” or the upstream head of the LSZ.  Another measure of the LSZ is X2, the heart of the LSZ, approximately 3800 EC.  The State Board has defined the Emmaton gage on the Sacramento River channel and Jersey Point gage on the San Joaquin River channel as the western edge of the Delta in terms of Delta agriculture and set wet year standards of a maximum 500 EC for the spring to fall irrigation season.  These standards have kept the LSZ out of the Delta in summer of wet years to the benefit of Delta agriculture and native fishes (and non-native striped bass).  However, the standard is also needed in the non-irrigation season when high Delta exports often occur.

Suggested measures to save the Delta:

  1. Do not allow south Delta exports to exceed a minimum (often prescribed as 1500 cfs) when Jersey Point and Emmaton gages exceed 500 EC.
  2. Place barriers on False River and Dutch Slough channels when their gages may exceed 500 EC.
  3. Open the Delta Cross Channel (DCC) to maintain a balanced EC at the Jersey Point and Emmaton gages and ensure positive outflow from the Delta at Jersey Point (often referred to as a positive QWEST). Closure of the DCC when EC rises at Jersey Point is detrimental to the LSZ when south Delta exports exceed 1500 cfs.
  4. Restrict Old and Middle River (OMR) negative flows to protect salmon and smelt from export facilities when these fish are in the interior Delta under freshwater conditions per biological opinions.
  5. Install or construct a permanent Head of Old River Barrier to keep San Joaquin salmon out of the south Delta in winter-spring under all export conditions.
  6. Increase San Joaquin River flows in the February-June time period.
  7. Keep Delta outflow at 8000-10,000 cfs in the fall after wet years to keep salt out of the Delta.

Example:  Water Year 2018

This new water year with its record November (wet) and December (dry) is a good example of what is wrong with the Delta.  Despite high reservoir levels for the beginning of a new water year1, Delta outflow was allowed to fall to 5000-7000 cfs in late November (Figure 1) as Delta exports literally sucked the freshwater bubble out of the Delta.  Exports averagedover 10,000 cfs from mid-November to mid–December, a time of year when there are no Delta controls.  The LSZ encroached at Emmaton (Figure 2), Blind Point (Figure 3), False River (Figure 4) on the west side of the Delta, Dutch Slough (Figure 5), and even showed up at the Rock Slough intake of the Contra Costa Water District in the south Delta (Figure 6).  See Figure 7 for the gage locations.

In conclusion, maintaining the 10,000 cfs Delta outflow necessary to keep the salt out of the Delta this past fall would have cost approximately 250,000 acre-ft of water from either the 18,000,000 acre-ft in storage or 1,500,000 acre-ft of Delta exports.  Doing so would have gone a long way toward protecting the past year’s production of winter-run smolts and pre-spawn Delta smelt that were both concentrated in the Delta.

Figure 1. Daily average Delta outflow for 11/7/17 to 1/4/18. Note each box-cell in chart represents approximately 7000 acre-ft of water. Maintaining a target 10,000 cfs to keep salt out of the Delta would have required an additional approximately 250,000 acre-ft of storage releases or export reduction.

Figure 2. The LSZ has encroached into the Sacramento River channel of the western Delta increasingly this water year. The limit should be 500 EC.

Figure 3. The LSZ has encroached into the San Joaquin River channel of the western Delta increasingly this water year. The limit should be 500 EC.

Figure 4. The LSZ has encroached into the central Delta via the False River channel from the western Delta increasingly this water year. The limit should be 500 EC.

Figure 5. The LSZ has encroached into the central and south Delta via the Dutch Slough channel of the western Delta increasingly this water year. The limit should be 500 EC.

Figure 6. The LSZ has encroached into the central and south Delta as seen at the Rock Slough gage of the south Delta increasingly this water year. The limit should be 500 EC.

Figure 7. Location of gages in above figures.

  1. As of December 1, Sacramento watershed reservoirs were 109% of average, and San Joaquin reservoirs were 150% of average. ↩