Category Archives: Water Quality

It is not too late for Delta smelt

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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.

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 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 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 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.

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

Spring 2016 Efforts to save Salmon in the Sacramento River below Shasta

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Management of flows and water temperatures in the upper Sacramento River near Redding for endangered salmon is frequently presented to the public as complicated, but it is really not that difficult to understand.  Chart 1 below depicts about everything that is involved with Sacramento River flows and their history so far this spring.  The box outlined in red indicates what has been wrong this spring.  The high temperatures shown in this box have hurt winter-run salmon, spring-run salmon, late-fall-run salmon, and green sturgeon, as well as fall-run salmon, steelhead, trout, and white sturgeon.  All of these species have suffered unnecessarily from this spring’s water management below Shasta.

Graph of Management of flows and water temperatures in the upper Sacramento River near Redding for endangered salmon is frequently presented to the public as complicated, but it is really not that difficult to understand. Chart 1 below depicts about everything that is involved with Sacramento River flows and their history so far this spring. The box outlined in red indicates what has been wrong this spring. The high temperatures shown in this box have hurt winter-run salmon, spring-run salmon, late-fall-run salmon, and green sturgeon, as well as fall-run salmon, steelhead, trout, and white sturgeon. All of these species have suffered unnecessarily from this spring’s water management below Shasta.

Chart 1. Latest update (6/9/16) from USBR on management of the upper Sacramento River below Shasta for winter-run Chinook salmon. The “spill” in late March was a managed flood release of over 200,000 acre-feet of storage, which kept Shasta (SHA) from filling (4.5 MAF). A key list of the location abbreviations pictured can be found in Table 1 at end of this post. A map of the locations is shown in Chart 3.

The red box in Chart 1 shows that water temperatures since April 1 have exceeded the 56°F target water temperature as defined in the State’s Sacramento Valley Basin Plan, the State’s Water Right Order 90-05 for Shasta Reservoir, and NMFS’s Biological Opinion for salmon and sturgeon as it applies to Shasta operations. These standards have been in place for many decades and are based on sound science.

In a March 31, 2016 letter to Reclamation1, a week after the flood control release from Shasta, NMFS stated: “Winter-run brood years in 2014 and 2015 experienced very low egg-to-fry survival to Red Bluff as a result of high water temperatures during their egg and alevin incubation stages. As brood year 2016 is the third of three winter-run cohorts, it is very important to operate Shasta Reservoirs conservatively to provide and maintain adequate water temperatures throughout the winter-run early life stages.” The letter concludes as shown immediately below:

Conclusion of NMFS Letter

So, within a week of the flood release, and based on a pre-spill March 15 forecast by Reclamation, NMFS changed the management compliance point to 55°F 7-day-average-daily-maximum at CCR (Bonneville Bridge in Redding) as a surrogate for a 56°F daily compliance at Balls Ferry (BSF) and Jellys Ferry (JLF). Note that Chart 1 above shows that this surrogate did not satisfy the requirements for either BSF or JLF. Note also that none of the flows prescribed in the table above for April (was 4700), May (6000), or June (7500 so far) have been met. (These flows should have been daily average minimum flows, not monthly averages.)

In an April 22 letter to Reclamation, the Pacific Fisheries Management Council recommended a 56°F compliance point at Jellys Ferry (JLF). That too has been exceeded in May and June.

In a May 2 letter, NMFS changed the compliance point to Keswick Dam: “We will continue to use the maintenance of 52°F daily average temperature (DAT) at Keswick Dam as an indicator of the ability to meet 55°F 7-day average of the daily maximum temperatures (7DADM) at the Bonnyview Bridge temperature compliance point (CCR CDEC location) throughout the temperature management season.” Note this new Keswick criterion was not met in late April or early May, but seems to be controlling after mid-May (Chart 1).

So why has there been so much compromise this spring (red box, Chart 1)? Why not simply meet the longstanding objective of keeping the daily average water temperature at Bend (BND) near Red Bluff? The reason is an unfounded fear by the managing agencies that they will run out of cold water in Shasta before the end of summer, as occurred in 2014 and 2015. Storage in Shasta in spring 2016 started with 4.2 maf. In contrast, storage in Shasta in spring 2014 and 2015 started out at 2.4 and 2.7 maf, respectively. Storage in Shasta in spring 2013 started out at 3.8 maf and met the standard. Storage in Shasta in spring 2009 started out at 3.2 maf and met the standard. There was more cold-water volume stored in Shasta this spring than the total spring storage in 2009 or 2013.

Between March 18 and March 28, 2016, a “flood release” of over 200,000 AF occurred, but the reservoir storage still rose from 3.9 to 4.0 maf. Most of the water released during the flood release was warmer surface water (Chart 2). Even then, the average water temperature from the surface outlets (upper gates) was only 48-50°F.

There is simply no information that indicates the reservoir will run out of cold water by the end of summer. Even Reclamation’s own conservative modeling indicates that a compliance point of 56°F at Balls Ferry can be met, which appears to be the present target in early June (Chart 1).

In conclusion, there is no reason why the Bend or at least the Jellys Ferry 56°F compliance point cannot be met. Perhaps more important is NMFS’s prescribed 9000 cfs June Keswick release. The lower release of 7500 cfs so far in June has resulted in (and allowed) the increased water temperature at Bend (and Red Bluff). These low flows and higher temperature (60-62°F at Red Bluff and higher downstream) have, in addition to adding stress on winter-run salmon, also jeopardized green sturgeon, white sturgeon, spring-run salmon, and steelhead (see previous post). Of the present 7500 cfs release, over 5000 cfs is diverted by downstream Sacramento CVP water contractors. An extra 2000 cfs Keswick release would increase mid-river flows at Wilkins Slough from the existing level of 3000-4000 cfs to 5000-6000 cfs, which would lower Water temperature at Wilkins at least several degrees from daily highs of 75-78°F, which are lethal to migrating adult salmon and young sturgeon.

Chart 2

Chart 2. Shasta Dam Temperature Control Device configuration on March 15, 2016.

Upper Sacramento Monitoring Stations

Chart 3. Map of key monitoring stations in upper Sacramento River below Shasta.

abbreviations list

Table 1. List of abbreviations for locations in Chart 1. A map of locations is shown in Chart 3 above.

Bay-Delta Spring Bloom Dissipates

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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 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”.

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 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 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.

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.

USBR – Increase Shasta Cold Water Releases

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Water Year 2016 on the Sacramento River has been designated a “Below Normal” year.  Water Year 2010 was also a Below Normal year.  Both years followed multiyear droughts.  In both years, Shasta Reservoir was nearly full at the end of April (2010 was 4.4 maf; 2016 was 4.2 maf).  In early May 2010, Keswick releases were 7500 cfs, and release water temperatures were 50-52°F.  In early May 2016, Keswick releases have been 5200-6200 cfs, and release water temperatures have been 53-55°F.

In April and May, 2010, water temperatures in the upper river remained below 56°F.  In contrast, the warmer, lower flows in 2016 have led to excessively warm water temperatures in the upper Sacramento River.  Water temperatures have reached 60-62°F in the upper river (Figure 1), which are well above the prescribed water quality standard of 56°F necessary to protect spawning salmon and sturgeon.  Winter-run salmon began spawning in late April.  Green and white sturgeon spawn in May.

Figure 1. Water temperature in the upper Sacramento River below Shasta Reservoir in early May 2016. In contrast, water temperatures at these locations during early May 2010 were 56°F or lower.

Figure 1. Water temperature in the upper Sacramento River below Shasta Reservoir in early May 2016. In contrast, water temperatures at these locations during early May 2010 were 56°F or lower.

Reclamation’s CVP operations should strive to maintain the 56°F standard through the spring and summer, as prescribed in the Basin Plan and in the NMFS biological opinion for Shasta operations. This temperature can be achieved by increasing Shasta releases or by lowering the water temperature of releases using the temperature control tower/device (TCD) at the dam, or by a combination of these elements. In the last few days, Reclamation has increased releases and has added colder water, resulting in slightly colder Keswick releases (Figure 1). Reclamation has decreased the temperature of releases by opening one the six middle outlets of the Shasta Temperature Control Device (Figure 2). However, downstream temperatures remain high, because air temperatures and water diversions downstream are also increasing.

While there is some logic behind Reclamation’s decision to minimize reservoir releases to save Shasta storage, it is inappropriate to jeopardize endangered fish in the upper Sacramento River with excessively warm water this year, given the abundance of cold water in the reservoir. 1

With Shasta releases expected to increase soon to meet increasing irrigation demands, it will be imperative that water temperatures upstream of Red Bluff remain below 56°F to protect spawning salmon and sturgeon and their young into and through the summer.

The “official” temperature target and control point since April 15, 2016 have been 58°F at Redding (station CCR). In 2010, the target temperature was 56°F, and the control point was at Jellys Ferry (RM 267), 20 miles downstream of Redding. The State Board and NMFS should immediately change the target temperature to 56°F, and move the control point at least downstream to Jellys Ferry. Preferably, the compliance point should be further downstream at Red Bluff, to be in compliance with the NMFS biological opinion (56°F at Red Bluff – RM 243). The Basin Plan puts the compliance point further downstream still, (56°F at Hamilton City – RM 200). 2

Following catastrophic losses of winter-run in the Sacramento below Shasta during the past two years, it is imperative to meet the summer water temperature goals as prescribed in the NMFS biological opinion. The Shasta cold-water pool and storage available are more than adequate to meet these objectives.

Figure 2. Shasta Dam’s temperature control tower/device or TCD has multiple options for releasing water from the reservoir. One middle outlet was recently opened to reduce the temperature of the water released to the Sacramento River. (Source: USBR MidPacific Division)

Figure 2. Shasta Dam’s temperature control tower/device or TCD has multiple options for releasing water from the reservoir. One middle outlet was recently opened to reduce the temperature of the water released to the Sacramento River. (Source: USBR MidPacific Division)

  1. A disproportionate amount of Sacramento River Delta inflow this spring has come from Oroville Reservoir (Feather River) and Folsom Reservoir (American River) storage releases. Excessive use of Folsom storage to meet Bay-Delta needs could lead to loss of its cold-water pool this summer and greater mortality of over-summering juvenile salmon and steelhead in the American River. ↩
  2. A plan for summer operations from Reclamation is due by May 15, 2016 ↩

Water Quality Standards Optional

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On May 5, I reported on the “chumming of stripers” with the late season release of millions of hatchery smolts into the warm, low flows of the Sacramento and Feather rivers.  So what more could the state and federal managers do to improve conditions for our salmon, steelhead, smelt, sturgeon, and other fish resources?    They could start by obeying and enforcing the rules already on the books.

Because of the restrictions placed on South Delta state and federal water project exports by rules governing San Joaquin River steelhead, exports are now restricted to no more than about 2500 cfs.  Such low exports at this time of year have in fact been the norm for the past 20 years under water quality standards and endangered species biological opinions.  The steelhead biological opinion for the San Joaquin is relatively restrictive this year because of the San Joaquin’s dry-year designation.

So what is the problem?  Because it cannot export, the US Bureau of Reclamation is releasing minimum flows from the warm surface waters of a full Shasta Reservoir.

This causes violations of the standards for Sacramento River water temperature.  The upper Sacramento River standard of 56°F has been violated: water temperatures have been running 60-62°F.  The lower river standard of 68°F has also been violated. water temperatures are running 70-72°F.  These conditions contribute to:

  1. Poor survival adult winter and spring run salmon in their peak migration perio;,
  2. Poor egg survival of winter run in the first month of spawning season;
  3. Poor late fall run salmon fry survival;
  4. Poor sturgeon egg survival during their peak spawning season; and
  5. Poor hatchery and wild smolt survival to the Bay.

The Delta outflow-salinity standard under D-1641 requires salinity at Chipps Island to be no more than 2.64 mmhos on a 14-day running average; the most recent 14-day average is above 3.0 mmhos.  With minimal Sacramento River inflow, Delta outflow has reached as low as 8,000 cfs in early May 2016.  These conditions contribute to:

  1. Poor migratory flows for adult and juvenile fall, winter, and spring run salmon, steelhead, and green and white sturgeon;
  2. Poor longfin and delta smelt survival; and
  3. Poor Delta and Bay productivity.

The standards (rules) governing the Central Valley rivers and Delta are there for a reason: to protect water quality, fish, and ecosystem function.  They do not contain the caveat: ‘Comply when convenient.’  They don’t have an exception that reads: ‘No Exports?  No Problem.  Release what meets your sense of order.’  With such gross disregard for the rules, it is no wonder our fisheries resources are in such a poor state.

Water temperature in past month at Bend Bridge near Red Bluff. Note: in 2010, the last below normal water year, water temperature did not exceed 58°F during first 12 days in May.

Water temperature in past month at Bend Bridge near Red Bluff. Note: in 2010, the last below normal water year, water temperature did not exceed 58°F during first 12 days in May.

River flow in past month at Wilkins Slough below Colusa on middle Sacramento River. Note: flow was 7000-13,000 cfs during first 12 days of May 2010, the last below-normal water year

River flow in past month at Wilkins Slough below Colusa on middle Sacramento River. Note: flow was 7000-13,000 cfs during first 12 days of May 2010, the last below-normal water year

Delta outflow in past month. Note: outflow in the first 12 days of May 2010, the last below normal year, was 20,000-30,000 cfs.

Delta outflow in past month. Note: outflow in the first 12 days of May 2010, the last below normal year, was 20,000-30,000 cfs.