San Joaquin River Spring-Run Salmon at Risk

Posted on April 11, 2018 by Tom Cannon

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.

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. ↩
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

Posted on April 5, 2018 by Tom Cannon

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

Posted on April 3, 2018 by Tom Cannon

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.

Where have all the salmon gone?

Posted on March 25, 2018 by Tom Cannon

Based on early indicators, it appears that salmon populations in the Central Valley are in critical condition. First, there was poor smolt production from the 2014 and 2015 drought-year salmon runs in the Central Valley. That led to last fall’s (2017) runs being so poor that Coleman Hatchery had to get eggs from state hatcheries on the Feather and American rivers to meet its needs.¹ CDFW believes poor ocean conditions have led to low adult salmon numbers for 2018 fisheries and runs. The weak runs may eliminate 2018 salmon fisheries. ²

The evidence based on initial surveys is that brood year 2017 salmon (born last summer and fall) fry-smolt production was extremely poor. First, lower Sacramento River screw trap catches are low in early 2018 compared to 2017 (Figures 1 and 2). Winter screw trap catch-per-trap-day (and Sacramento trawl catch not shown) in the lower Sacramento River in 2018 are only 2% of 2017. Note flows and turbidities were very low in 2018 compared to 2017. I warned that these conditions with warmer water would lead to slower migration rates, starvation, and high predation by stripers. Second, salmon salvage at the south Delta pumping plants has been extremely low in 2018 (Figure 3) compared to 2017 (Figure 4). Salvage is a strong indicator of relative abundance. Third, compared to historical levels (Figure 5), salvage numbers in 2018 are two orders of magnitude lower than in 1999 when salmon runs were last strong.

You can blame the problem on the 2012-2016 drought, poor ocean conditions, or poor river-Delta flow management as I do. Whatever the cause, strong measures are needed to recover the salmon populations. Without strong measures, future brood year production will be so low there will be few salmon and no salmon fishing.

Figure 1. Knights Landing screw trap catch Aug 2017 to Mar 2018.

Figure 2. Knights Landing screw trap catch Aug 2016 to Aug 2017.

Figure 3. Chinook salmon salvage at CVP fish facilities in south Delta Nov 2016 to March 2018, along with export rate at Jones Plant. Note very small, nearly unperceivable numbers in winter 2018.

Figure 4. Chinook salmon salvage at SWP fish facilities in south Delta Nov 2016 to March 2018, along with export rate at Clifton Court. Note very small, nearly unperceivable numbers in winter 2018.

Figure 5. Chinook salmon salvage at CVP and SWP fish facilities in south Delta Jan 1999 to June 1999, along with export rate at south Delta pumping plants.

Winter-Run Chinook Salmon – What Really Caused Their Decline

Posted on March 14, 2018 by Tom Cannon

The winter-run Chinook salmon population crashed around 1980 and has not recovered (Figure 1). The population started coming back from 2001-2006 but fell to 827 in 2011. It remained in the 1500 to 6000 range from 2012-2016¹ with the help of the Livingston Stone federal hatchery near Redding. Hatchery fish make up an increasing proportion of the population each year.

In a 2011 review, NMFS attributed the general population decline to “blockage of access to historic habitat, other passage impediments, unscreened water diversions, heavy metal pollution from mine runoff, disposal of contaminated dredge sediments in San Francisco Bay, ocean harvest, predation, drought effects, juvenile losses at the CVP and SWP Delta pumping facilities; and elevated water temperatures in spawning grounds.” Droughts and the loss of cold water pool in Shasta are generally considered the primary cause of the decline over the past four decades starting with the 1976-1977 drought. The decline continues despite “reduced harvest impacts, Iron Mountain Mine clean up, screening of water diversions, altered CVP water operations that improve passage and reduce predation, and construction of a temperature control device on Shasta Dam”.

A range of actions is being implemented to help recover this NMFS-designated “Species in the Spotlight.” The problem is the actions do not include the one key factor that was a major cause of the original decline and the primary cause of the lack of recovery: high late-fall and early-winter Delta exports cause high juvenile salmon mortality in the Delta.

The problem starts from the fact that winter-run juveniles leave the upper Sacramento River rearing area for the Bay-Delta and eventually the ocean with the first fall or early winter rains that produce flow pulses from undammed Sacramento River tributaries. These same untamed flows are also a primary target of the state and federal export facilities in filling south-of-Delta storage depleted from the summer. Delta exports have few restrictions in fall. The allowed export-to-inflow ratio is 65% (compared to 35% in winter-spring). There are no OMR limits. Interior Delta flows caused by high exports reach -10,000 cfs, compared to -5000 cfs in winter-spring. The Delta Cross Channel is usually open through the fall and closed in winter, allowing salmon to move from the Sacramento River to the interior Delta more easily in fall. Higher fall exports are also a consequence of increasing winter-spring protections (in water quality control plans and endangered fish biological opinions) for fish that led to reduced exports in those seasons. Fundamentally, higher fall exports were a result of the state export facilities coming on line in the mid-1970s, which increased the export capacity from 4,400 cfs to 15,000 cfs.

One need only look at the increase in fall export rates and juvenile salmon salvage in the south Delta to see the association with the decline of winter-run. Figure 2 shows CVP exports in 1984-1985 compared with the historical average. Figures 3 and 4 show fall exports in the example years. Figure 5 shows fall 2016 exports and Delta inflow, which is compelling proof that the problem continues.² Figure 6 shows high negative Old and Middle River (OMR) flows caused by high exports. Figure 7 shows December Chinook salmon salvage at south Delta fish facilities. Further evidence of the association between fall exports and the decline of winter-run is available in the long-term fish salvage data that dates back to the 1970s historical period depicted in Figure 1. Further discussion on the risk of high fall and early winter risks to salmon from exports is presented in http://calsport.org/fisheriesblog/?p=1949 .

Figure 1. Trend in winter-run salmon escapement to the Sacramento River below Shasta Reservoir 1970-2009 in thousands of adult salmon. Source

Figure 2. Tracy (federal) export rate in 1984-1986, with mean daily export rate 58-year average. Note marked increase in Nov-Dec period over historical average.