It is not too late for Delta smelt

Posted on June 16, 2016 by Tom Cannon

Before the 2012-2015 drought, Delta smelt had a recovery period in 2010 and 2011. Now, in 2016, there remains an opportunity for some form of recovery, albeit small. What is needed is exactly what the US Fish and Wildlife Service has been pleading for so far this spring to save Delta smelt: more Delta outflow.

This note was at the bottom of the USFWS’s last Delta smelt determination memo to the USBR on June 1, 2016. This literally was their last action this year under the Delta Smelt Biological Opinion because there are no protections in summer once the South Delta reaches a water temperature of 25°C (77°F).

This note was at the bottom of the USFWS’s last Delta smelt determination memo to the USBR on June 1, 2016.¹ This literally was their last action this year under the Delta Smelt Biological Opinion because there are no protections in summer once the South Delta reaches a water temperature of 25°C (77°F).

A careful look at the four figures below indicates that there remains a chance to recover smelt this summer. There is a concentration of Delta smelt near Sherman Island in the west Delta (figure 1). If these smelt can get to Suisun Bay in the coming weeks as they did in 2010 and 2011, where habitat is better and where they are away from the influence of the south Delta exports, then they have a chance.

To move the largest remaining concentration of this species in existence downstream, it will take outflows of about 10,000 cfs. Right now outflows are about 7500 cfs (see chart 1, below), the minimum required under present water quality standards. The fisheries agencies and the water projects need to find a way to make up the difference as soon as possible.

Chart 1. Delta outflow in June 2010, 2011, 2015, and 2016. 2011 was a Wet year. 2010 and 2016 are Below Normal water years. 2015 was a Critically Dry year.

Figure 1. Mid-June 20-mm Smelt Survey 2016. Largest green dot is in north side of Sherman Island in Sacramento River channel of west Delta.

Figure 2. Mid June 20-mm Smelt Survey 2010. Note smelt length-frequency chart at bottom-center of chart, which also depicts total caught in survey.

Figure 3. Mid-June 20-mm Smelt Survey 2011.

Figure 4. Mid-June 20-mm Smelt Survey 2015. Large green dot is in Sacramento Deep Water Ship Channel.

https://www.fws.gov/sfbaydelta/documents/smelt_working_group/ R8_Signed_Determination_Memo_to_BOR_06-01-2016.pdf ↩

Spring-Run Chinook Salmon – why they fail to recover

Posted on June 10, 2016 by Tom Cannon

Spring-run are the most prized of the four runs of Central Valley, West Coast, and Alaska Chinook because they leave the ocean with the biggest stores of fat energy and strength to sustain them through to spawning. They are prized for sport and table value.

Spring-run are perhaps best adapted of the four runs to California’s Central Valley because they migrated upstream with the snowmelt in spring. Dependable high cold flows allowed access to colder-summer mountain habitats. Yearling smolts emigrated to the ocean in the same snowmelt period.

Construction of rim dams captured the snowmelt and blocked migrations, leading to dramatic declines in run size. Runs were confined to a few un-dammed streams (e.g., Mill and Deer creeks) or below dams (e.g., Shasta Dam). Reservoir storage and water diversions in many Valley streams further blocked migrations and reduced flows (Chart 1) and raised water temperatures.

Central Valley runs that once numbered in the hundreds of thousands or more are now down to a few thousand. Multimillion dollar efforts have been underway now for several decades to restore spring-run. The spring run goal for the Central Valley Project Improvement act of 1992 is 59,000 spring-run below Shasta in the Sacramento River. The average run size from 1992-2012 was 684. The primary reason for lack of recovery is low flow and high water temperatures in spring in the lower Sacramento River and spawning tributaries. No river or creek has been unaffected, and so the spring-run have rapidly declined. (See references for early reports on spring-run and their decline.)

Peak migration of adult spring-run Chinook into the upper Sacramento occurs in May and June.¹ About 80% of the spring-run passes Red Bluff after May 15. The adults oversummer in the upper Sacramento River and its tributaries before spawning in September and October. During migration and oversummering they require cold-water habitat for survival and the maturation of their gonads. Lack of cold water habitat reduces the viability of their eggs and sperm and subjects adults to poor survival from disease, energy loss, and heat stress.

Chart 1. Example of spring snowmelt being captured by dams – Feather River. (Source: NHI 2008²)

Of the four runs, spring-run are also the hardest to recover. The main reason is because they migrate from the ocean to their spawning rivers in spring, they are increasingly at risk to warm spring water temperatures in the lower Sacramento River. Water temperatures of 70°F or higher are detrimental to migrating salmon, and spring-run are especially at risk because much of the Valley’s cold snowmelt is captured and held in rim dam reservoirs. Those spring-run headed for un-dammed tributaries must still pass through the lower Sacramento River. NMFS’s criteria that define water temperature habitat degradation are shown in Chart 2 below. Water temperatures above 65°F are unsafe for salmon migration. In the Basin Plan the water temperature standard set by the State for the lower Sacramento River is 68°F to protect migrating salmon and other cool-water dependent fish (e.g., sturgeon and steelhead). Water temperatures of 72-74°F can block or severely delay migration.³ An excellent review of water temperature requirements of salmon by CDWR and Stillwater Sciences⁴ describes water temperatures above 65°F as being detrimental to migrating spring run salmon.

Chart 2. Aquatic life temperature criteria for freshwater. 7DADMax is the seven running average of the daily maximum water temperature. 1-Day Maximum is the daily average water temperature. (Source: NMFS).

Water temperatures typically exceed 68°F in spring in the lower Sacramento River (Charts 3 and 4). In drier years high water temperatures may even block migration (72-74°) or kill adult salmon (>75°F). The high spring water temperatures are due in large part to low flows above (3000-5000 cfs) and below (5000-7000 cfs) the mouth of the Feather River at Verona (RM 80). A closer look at 2016 at Wilkins Slough (Charts 5 and 6) and Verona (Charts 6 and 7) show the relationship between flow and water temperature. While air temperatures and tributary water temperatures (particularly the Feather River at Verona) likely also played a part in patterns observed, the overall pattern from 2008 to 2016 indicates higher water temperature are a consequence of low river flows. Flows of 10,000 cfs and higher in May-June of 2010 and 2011 led to to water temperatures below 65°F. Intermediate flows (8000-10,000 cfs) in May-June 2012 and 2013 led to water temperatures from 68-70°F.

The issue of low river flows and high water temperatures in spring has received little consideration in drought management plans, salmon biological opinions, and the NMFS Central Valley Recovery Plan. The only consistent attention has been centered around reducing Shasta releases and lowering flows at Wilkins Slough to save Shasta storage and cold-water pool in dry years. Even this spring, with a full Shasta Reservoir, the overwhelming concern for saving the Shasta cold-water pool has led to minimum releases and Wilkins Slough flows near 3000 cfs. Mention is rarely made of meeting the Basin Plan 68°F criterion for the lower Sacramento River. If anything was mentioned, it was for allowing a reduction in spring flows below Keswick and at Wilkins Slough to 3000-4000 cfs to save Shasta storage and cold-water pool. Most of the required water for Delta inflow has come from the Feather and American Rivers.

Another problem rarely mentioned is warm water discharges, especially agricultural drainage into the lower Sacramento River in spring. Water temperatures from these considerable sources can easily exceed 80°F. The Knights Landing Outfall of the Colusa Basin Drain is one such source. I once measured 80°F on May 1 at the mouth of the Feather River during the peak season of the Feather’s substantial spring-run.

The operations that imperil spring-run create a serious issue that deserves much more attention. Increasing Wilkins Slough flows by several thousand cfs would go a long way to reducing this year’s problem. This would require up to 200,000 acre-ft of Shasta storage, or about 5% of the 4.2 maf of present storage. The added flow would help maintain winter-run spawning near Redding in June and improve Delta inflow/outflow and perhaps exports. At present, 7,000 cfs is being released at Keswick, with only 3000 cfs reaching Wilkins Slough. The difference is being diverted from the upper river by CVP water contractors.

Chart 3. Water temperature of the Sacramento River at Wilkins Slough (RM 125) from May 2008 to early June 2016. Higher water temperature in May-June 2014 and 2015 drought years and 2016 occurred at May flows of 3000-5000 cfs.

Chart 4. Water temperature of the Sacramento River at Verona (RM 80) from May 2008 to early June 2016. Higher water temperature in May-June 2014 and 2015 drought years occurred at flows of 5000-7000 cfs.

Chart 5. Water temperature of the Sacramento River at Wilkins Slough (RM 125) from May to early June 2016.

Chart 6. Flow in the Sacramento River at Wilkins Slough (RM 125) from May to early June 2016.

Chart 7. Water temperature of the Sacramento River at Verona (RM 80) from May to early June 2016.

Chart 8. Flow in the Sacramento River at Verona (RM 80) from May to early June 2016.

References

Hallock, R.J. 1983. Sacramento River king salmon life history patterns a t Red Bluff, California. Unpubl. Central Valley Project report, California Department of Fish and Game, Red Bluff.

Hallock, R.J.., and D.H. Fry. 1967. Five species of salmon, Oncorhynchus, in the Sacramento River, California. Calif. Fish Game 53:5-22.

Hallock, R.J., and W. F. Van Woert. 1959. A survey of anadromous fish losses in irrigation diversions from the Sacramento and San Joaquin Rivers, Calif. Fish Game 45:227-296.

Hallock, R.J., R.F. Elwell, and D.H. Fry. 1970. Migrations of adult king salmon, Oncorhynchus tshawytscha, demonstrated by the use of sonic tags. Calif. Fish Game Fish Bull. 151. 92 pp.

Anadromous Fish Restoration Program of CVPIA – http://www.fws.gov/stockton/afrp/

Yoshiyama, R. M., F. W. Fisher, and P. B. Moyle. 1998. Historical abundance and decline of Chinook salmon in the central valley region of California. North American Journal of Fisheries Management. 18(3):487–521. ↩
http://www.n-h-i.org/uploads/tx_rtgfiles/FINAL_Sacramento_and_Feather_Env_Flows_Doc.pdf ↩
http://www.tandfonline.com/doi/abs/10.1577/T09-171.1?journalCode=utaf20 ↩
http://www.water.ca.gov/pubs/environment/fish/ upper_yuba_river_watershed_chinook_salmon_and_ steelhead_habitat_assessment/yuba_salmon.pdf ↩

End of May 2016 Smelt Update

Posted on June 5, 2016 by Tom Cannon

Since my last update in April, Delta and longfin smelt have continued their trends of record low numbers. I opined that they were not yet gone, but close, and that it remained to be seen whether the good conditions provided to date in 2016 could lead to some form of recovery for these two endangered species. The prognosis remains poor.

Habitat conditions in the Bay-Delta remained good through April and May. Below normal year estuary inflows were modest, and Delta exports were low thanks to caps in endangered fish species biological opinions. Longfin and Delta smelt may have further benefitted from a rare spring plankton bloom.

A quick view of the status of smelt can be gleaned by comparing recent May 20-mm Survey results with those from last year, the fourth year of drought conditions, and those from 2010, the last below normal water year before the 2012-15 drought and after the 2007-09 drought.

Longfin Smelt

The May 2016 survey (Figure 1) compares favorably with the 2015 Longfin pattern (Figure 2), but less so with 2010 (Figure 3). Higher densities of longfin smelt occurred in Suisun Bay this year compared to 2015, although they are generally lower than in 2010. Year 2010 had higher Delta outflow in spring, and longfin juveniles had a wider distribution and higher densities.

Delta Smelt

The May 2016 survey (Figure 4) shows little or no improvement in Delta smelt compared with 2015 (Figure 5), and poorer performance when compared to 2010 (Figure 6). Most of the young Delta smelt in 2015 and 2016 were confined to the Sacramento Ship Channel in the north Delta, whereas in 2010 they were more widely distributed into the western Delta and Suisun Bay, albeit in very low densities compared to historical levels.

Map of Longfin smelt young densities from May 2016 20-mm Survey

Figure 1. Longfin smelt young densities from May 2016 20-mm Survey. Source of charts: https://www.wildlife.ca.gov/Conservation/Delta/20mm-Survey

Map of Longfin smelt young densities from May 2015 20-mm Survey

Figure 2. Longfin smelt young densities from May 2015 20-mm Survey.

Figure 3. Longfin smelt young densities from May 2010 20-mm Survey.

Map of Delta smelt young densities from May 2016 20-mm Survey.

Figure 4. Delta smelt young densities from May 2016 20-mm Survey.

Map of Delta smelt young densities from May 2015 20-mm Survey

Figure 5. Delta smelt young densities from May 2015 20-mm Survey.

Map of Delta smelt young densities from May 2010 20-mm Survey

Figure 6. Delta smelt young densities from May 2010 20-mm Survey.

Bay-Delta Spring Bloom Dissipates

Posted on May 31, 2016 by Tom Cannon

In a May 17 post I discussed the occurrence of a rare spring Bay-Delta plankton bloom. The bloom coincided with moderate Delta inflow and outflow in the present “normal” water year combined with a pulse of Delta inflow from the San Joaquin River. The bloom and associated conditions likely benefitted smelt, salmon, striped bass, and other Bay-Delta fishes by providing cover (turbidity) and food for young fish.

The bloom has now dissipated in the Delta and Suisun Bay (Figures 1-3). In contrast, the bloom has continued to intensify in the San Joaquin River upstream of the Delta (Figures 4 and 5). The dissipation of the bloom coincided with the cessation of the San Joaquin pulse flow (2500-3500 cfs from April 18-May 15) combined with Delta inflow and outflow that is increasingly dominated by low turbidity, low nutrient water from the Sacramento River (Figure 6), mainly from high seasonal storage releases from Oroville (Feather River) and Folsom (American River) reservoirs. In addition, with total South Delta exports now between 2000-3000 cfs, most if not all of the remaining turbid, high nutrient San Joaquin bloom water is being exported before it reaches the central Delta.

This pattern of Delta hydrology in a “normal” Sacramento River water year and a “dry” San Joaquin River water year shows the importance of the nutrient-laden San Joaquin water in the overall productivity of the Bay-Delta estuary.

Figure 1. Chlorophyll concentration May 12-27, 2016 in the lower San Joaquin River channel of the Delta east of Antioch near Sherman Island. Concentrations above 10 micrograms per liter of water are considered indicative of high phytoplankton production – a “bloom”. Source: CDEC.

Figure 2. Chlorophyll concentration April 27-May 25, 2016 in the lower Sacramento River channel of the Delta north of Antioch adjacent to Sherman Island. Concentrations above 10 micrograms per liter of water are considered indicative of high phytoplankton production – a “bloom”.

Graph of Chlorophyll concentration April 28-May 27, 2016 in eastern Suisun Bay at Chipps Island near Pittsburg, CA

Figure 3. Chlorophyll concentration April 28-May 27, 2016 in eastern Suisun Bay at Chipps Island near Pittsburg, CA. Concentrations above 10 micrograms per liter of water are considered indicative of high phytoplankton production – a “bloom”.

Figure 4. Chlorophyll concentration April 28-May 27, 2016 in San Joaquin River upstream of the Delta at Mossdale Bridge.

Figure 5. Chlorophyll concentration April 28-May 27, 2016 in San Joaquin River upstream of the Delta at Vernalis.

Figure 6. The relative proportions of Delta inflow from the Sacramento and San Joaquin rivers in May 2016. The higher proportion of San Joaquin inflow in the first half of May was from a flow pulse. Higher Sacrament River flows after early May are from increased storage releases from Oroville and Folsom reservoirs.

Rare Bay-Delta Spring Bloom may benefit Smelt

Posted on May 17, 2016 by Tom Cannon

A rare Bay-Delta spring plankton bloom in 2016 may benefit longfin and Delta smelt (and other fish). The bloom (a condition in which chlorophyll concentrations consistently exceed 10 micrograms per liter of water) commenced in late April. Geographically, it extended from Suisun Bay up into the Delta to Rio Vista on the Sacramento River and to near Stockton on the San Joaquin River (Figure 1).

Figure 1. Bay-Delta phytoplankton bloom late-April to mid-May 2016. Plots show chlorophyll concentrations at selected stations from mid-April to mid-May. Source: CDEC.

The bloom coincided with a drop in previously high early spring Delta inflow and outflow, as well as with low exports and the implementation of San Joaquin River pulse flows.¹ Delta outflows were moderate, relatively steady, and higher than in recent drought years, and consistent with a “normal“ year pattern (Figure 2). San Joaquin River pulse flows occurred after mid-April (Figure 3). The Low Salinity Zone or LSZ (0.5-6 ppt) was located in Suisun Bay. X2 (2 ppt) migrated with the tides from Honkers Bay (northwest of MAL) to Sherman Island (northeast of ANH) within eastern Suisun Bay. The head of the LSZ (500-1000 EC) and the bloom extended upstream to Rio Vista on high tides (Figures 4 and 5). Water quality standards (D-1641) that require 14-day average X2 to be at Chipps Island (MAL) or further west helped to ensure consistent Delta outflow.

Longfin smelt concentrated near X2 and may benefit from plankton bloom (Figure 6). Remaining Delta smelt may also benefit as they too concentrate near X2. Maintaining the LSZ and X2 in Suisun Bay is generally thought to promote Bay-Delta productivity and higher smelt survival. In the past four years of drought, the LSZ and X2 during spring and summer have generally been upstream of Suisun Bay, in the Delta.

Figure 2. Delta outflow mid-April to mid-May 2016. Source: CDEC.

Figure 3. San Joaquin River inflow to the Delta at Mossdale April-May 2016. Source: CDEC.

Figure 4. Bottom salinity in Sacramento River several miles downstream of Rio Vista in early May 2016. Source: CDEC.

Figure 5. Chlorophyll concentrations at Rio Vista in early May 2016. Source: CDEC

Figure 6. Catch distribution of young Longfin smelt in late April 2016 along with extent of plankton bloom (red boundary). Smelt were concentrated (larger green dots) near X2 in central and eastern Suisun Bay. Source: CDFW 20-mm Survey.

The bloom also occurred after a winter of moderate Yolo Bypass flood spills that may have contributed nutrients to fuel the bloom. Elevated Bypass flows continued through mid-April. ↩

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