Welcome to the California Fisheries Blog

The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.

Delta Smelt Spawning Run – Record Low February 2018 Index

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Despite three straight non-drought winters (2016-2018) the Delta smelt spawning run shows no sign of recovery based on the Kodiak Trawl Survey (Figure 1). The February 2018 survey brought a record low catch of only 4 adults (compared to 125-287 from 2011-2013). The March index was “1”. As in my last post, the prognosis for Delta smelt remains grim. The next check is the spring 20-mm Smelt Survey index to determine if this years spawning run production of juvenile smelt continues the pattern of four years of near record lows (Figure 2).

Figure 1. Kodiak Trawl Survey catch of Delta smelt in winter 2002-2018. Source: CDFW survey data.

Figure 2. CDFW 20-mm Survey Delta smelt index 1995-2017. Source: https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=147044

 

Miracle March/April for Water Supply and Fish

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It has been a “Miracle March-April” for water supply and fish in the Central Valley. Over 2 million acre-feet of water was added to Central Valley storage reservoirs. Many major reservoirs reached flood capacity, with large releases and rivers spilling over into flood bypasses. The snowpack doubled to over 50% of average. Water year 2018 cumulative precipitation nearly doubled (remains 10 inches short of average at about 80% of normal).1 Water Year 2018 will likely stack up as “below normal,” not unlike 2010, 2012, or 2016.

Without the added precipitation so far this spring, water conditions would be similar to critically dry 2015. The prognosis for salmon, smelt, and sturgeon would be poor with yet another drought year. The fish have yet to recover from the 2012-2016 drought.

In the next three months, tens of millions of wild and hatchery juvenile salmon and steelhead will be leaving Valley rivers for the Delta, Bay, and ocean. Millions of young smelt and sturgeon will be trying to reach their Bay low salinity nurseries. Adult fall, winter, and spring run salmon and green and white sturgeon will be seeking their upriver spawning grounds. All of these populations are in real trouble and need help after years of stress.

Some of the Miracle March-April water added to Central Valley storage should be set aside for the fish. Fish need higher river flows and Delta outflow through summer than would normally be allocated in a sub-normal water year like this. Lower Sacramento River flows (Figure 1) should be kept near 8000 cfs, not the projected 5000-6000 cfs. San Joaquin River flows should be kept near 1000 cfs (Figure 2). The Delta outflow minimum should be 8000 cfs (Figure 3), not 5000 cfs, by allowing the added river flows to pass through the Delta. The “extra” water would amount to about a quarter of Mother Nature’s gift to the reservoir supply added so far this spring. That would seem more than reasonable and fair. In most cases it means meeting already prescribed flow and water temperature standards for the Central Valley rivers and Delta. These standards have been more than regularly ignored in recent years. So let’s do the fish a favor for once – call it “adaptive management” – and see if it helps.

Figure 1. Flow in lower Sacramento River at Wilkins Slough over past decade.

Figure 2. Flow in lower San Joaquin River at Vernalis over past decade.

Figure 3. Delta outflow at Pittsburg over past three years.

San Joaquin River Spring-Run Salmon at Risk

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Give them a chance.

Soon after spring run salmon smolts were released from the new San Joaquin River Spring-Run Recovery hatchery at the beginning of March, they began appearing in south Delta export salvage facilities (Figure 1). The number salvaged is unusually large, about one percent of the 87,000 released1, in salvage historical records as indicated in Figure 1. The salvage rates of recovery for the other winter 2018 Central Valley hatchery releases are much lower. The high rate of salvage of the March 1 San Joaquin River spring-run release reflects the vulnerability of young salmon that are drawn into the south Delta, where they are at risk to the State Water Project (SWP) and Central Valley Project (CVP) export facilities.

That risk comes from high export levels in winter-spring. Salvage of the spring-run smolts increased sharply as combined SWP and CVP exports reached high levels (8000-10,000 cfs) in late March (Figure 2). Such high exports were allowed this spring because of the increase in San Joaquin flows in late March (Figure 3). Tying export limits to San Joaquin flows2 and OMR flows is obviously not protecting San Joaquin salmon emigrants. The flow pulse may be the trigger that moves the young salmon down to the Delta. Exports should be reduced, not increased, during such pulses. But both current requirements as prescribed in the OCAP Biological Opinion for the Delta operations and requirements proposed under WaterFix allow increasing exports as flows increase.

Figure 1. Salvage of salmon at south Delta export fish facilities August 8, 2017 to April 5, 2018.

Figure 2. Salmon salvage and export rates from state and federal export facilities in south Delta March 1, 2018 to April 5, 2018.


Figure 3. San Joaquin River flow at Mossdale December 10, 2017 to April 7, 2018.

  1. Note: the actual rate of tagged fish recovered is much higher because salvage numbers are estimated from subsamples, and many fish are lost in Clifton Court Forebay prior to reaching salvage facilities. ↩
  2. Exports are also limited by Old and Middle River negative flow limits (-5000 cfs), which were exceeded in late March ↩

Salmon Spring Threat – Need for Strong Measure

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In a March 25, 2018 post, I suggested strong measures to protect salmon populations in the Central Valley. Well, it is time for action number one. Young salmon from last fall’s spawn are pouring down the rivers for the Delta, Bay, and ocean. Hatcheries are about to stock millions of fall-run smolts. Up until last week, young salmon were getting lots of roiling cold water to push them along on their journey. But with a break in the rains snow melt is being trapped in reservoirs, and things are changing. Waters are getting warmer, fish are getting stressed, and predation is up. Sacramento River water levels have dropped over ten feet in the past week, and flow has dropped by half (Figure 1). Water temperatures below Colusa have risen sharply to over 60°F, perfect to stimulate the appetites of striped bass.

Figure 1. River flow at Wilkins Slough on lower Sacramento River, March 26-April 1 2018.

Over the next six warm months, April through September, state water quality standards are supposed to assure salmon of cold 56°F water at Red Bluff and cool 68°F water from there down to the Delta. Outmigrating young salmon need cool water. Newly hatched sturgeon need the cool water in spring. Adult winter-run and spring-run salmon also require the cool water during their spring upstream migration. Adult fall-run salmon need the cool water during their upstream migrationin the late summer and fall.

Until a few years ago, the fish were usually provided what they needed, even in a drought year like 2013 (Figure 2). But that changed during the 2013-2015 drought. In 2015, water temperature reached above 68°F by late April and near 80oF in the summer. (Figure 3). In below-normal water year 2016 and wet water year 2017, low Shasta releases and high water temperatures continued (Figures 4 and 5), to the great detriment of salmon and other native fishes like steelhead and sturgeon.

Now, in spring 2018, conditions have already deteriorated quickly. Water temperatures at Red Bluff now exceed 56°F (Figure 6). Soon lower river water temperatures will reach above 65°F.

The answer is simple. At minimum, Reclamation should keep the flow of the lower Sacramento River at Wilkins Slough near 8000 cfs, as in 2013. Shasta Reservoir is 88% full, 105% of average, and the reservoir will likely fill (4.5 million acre-ft) this spring. Federal managers and contractors probably are forecasting a spring flow of 5000-6000 cfs in the Sacramento River at Wilkins Slough, similar to last year. That would save Reclamation 240,000-360,000 acre-feet in Shasta over two months. But the extra storage would come at the expense of water quality and fish standards, and would mean a lot fewer salmon for the future.

Figure 2. Wilkins Slough gage spring-summer flow and water temperature 2013. Green line is 65°F stress limit for salmon. Red line is water quality standard 68°F for lower Sacramento River.

Figure 3. Wilkins Slough gage spring-summer flow and water temperature 2015. Green line is 65°F stress limit for salmon. Red line is water quality standard 68°F for lower Sacramento River.

Figure 4. Wilkins Slough gage spring-summer flow and water temperature 2016. Green line is 65°F stress limit for salmon. Red line is water quality standard 68°F for lower Sacramento River.

Figure 5. Wilkins Slough gage spring-summer flow and water temperature 2017. Green line is 65°F stress limit for salmon. Red line is water quality standard 68°F for lower Sacramento River.

Figure 6. Water temperature at Bend Bridge near Red Bluff in 2018.

Merced River Salmon

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The Merced River salmon population trends follow a similar pattern to those of other Central Valley rivers (Figure 1). Droughts (76-77, 87-92, 07-09, and 13-15) drive the population down. The basic response appears as a two year lag, reflecting the fact that primary mortality comes in the first year of life while living in rivers and migrating to the ocean. Lack of lag in some years likely reflects poor river conditions in late summer and fall when high mortality of adults may occur during their spawning run. The population increases in normal-wet year sequences (82-86, 95-00, and 10-12). The recent better drought performance with good runs in 2016 and 2017 (not shown) likely reflects the practice of trucking most of the Merced Hatchery smolts to the Bay in spring since 2010.

High trucking survival, especially in dry years, is indicative of the real problem facing Merced, San Joaquin, and Sacramento River salmon: poor river habitat conditions downstream of the hatcheries and upper river spawning grounds. One only has to look at water temperatures and flows in the lower San Joaquin River in winter-spring to see that survival conditions are poor in spring, especially in drier years.

With 2017 being a wet year, Merced Hatchery fall run smolts were released in spring at the hatchery outlet instead of being trucked to Bay pens. Approximately 1,250,000 smolts were released in three groups: 4/24, 5/3, and 5/18 (Figure 2). The problem with these releases even in a wet year like 2017 is warm water in the San Joaquin River below the mouth of the Merced River (Figure 3). In dry years like 2015, water temperature are are even higher and occur earlier in spring, with lethal temperatures (>770F) occurring by late April (Figure 4). This is the reason why the hatchery trucks smolts to the west Delta in dry years.

Looking at the most recent tag return data (Figure 5), it appears that trucking to the Bay or west Delta is the best course of action even in wet years like 2011. Because smolts were released at the hatchery in wet year 2017, a poor return would be expected in 2019. A good return is expected in 2018 because smolts were trucked in 2016. Based on these data, trucking would be the best choice in all years.

Merced hatchery smolts are expected to be released later this spring. DFW should truck these smolts to the west Delta. This is particularly important because since 2011, spring Delta exports have been higher than they generally were over the previous three decades. During the Vernalis Adaptive Management Program (VAMP) from 1999 through 2010, April 15 – May 15 exports were restricted to 1500 cfs. Higher spring export levels since the end of VAMP are a real threat to Merced and other Central Valley salmon populations (Figure 6).

Figure 1. Merced River salmon run (escapement to river) 1975-2016. Source: CDFW GrandTab.

Figure 2. Summary of salmon salvage at south Delta pumping plants in winter-spring 2017. Note three Merced hatchery smolt release groups reached the south Delta salvage facilities in early May and continued to be salvaged into mid June. Only 20% of Merced hatchery smolts were tagged, so many of the non-marked smolts at that time were likely also hatchery smolts. Source: http://www.cbr.washington.edu/sacramento/tmp/deltasalvagelength_1521657439_409.html

Figure 3. Water temperature in the San Joaquin River below the mouth of the Merced River at Crows Landing in spring 2017. Red line is high stress level that would lead to poor growth and survival, and high rates of predation. Green line is upper end of optimal growth potential. Yellow line is moderate stress level.

Figure 4. Water temperature in the San Joaquin River below the mouth of the Merced River at Crows Landing in spring 2015, a critically dry year. Red line is high stress level that would lead to poor growth and survival, and high rates of predation. Green line is upper end of optimal growth potential.

Figure 5. Adult hatchery salmon return percentage from tagged smolts released from 2007 to 2013 at the hatchery or trucked to the west Delta. Data Source: http://www.rmis.org/ .

Figure 6. May 2017 salmon salvage at south Delta export facilities with export cfs. Data source: CDFW.