Salmon Season Opens July 16

Posted on July 2, 2016 by Tom Cannon

The Sacramento River salmon season opens on July 16 in the lower Sacramento River below Red Bluff, and in the lower Feather and American Rivers, as well as in the Bay-Delta. Will the Sacramento River remain cold enough to allow the fall-run salmon to leave the Bay and Delta for the rivers? Are the lower rivers warming into the 72-75°F range that blocks migration and stresses the adult salmon?

Salmon will be headed for the upper river reaches where water temperatures are cool, near 60°F. The Bay and west Delta remain below 70°F. At Rio Vista and Freeport on the Sacramento River in the north Delta water temperature have reached 70°F and are slowly rising. Upstream of the Delta, downstream of the points of relatively cool inflow from the Feather and American rivers, the Sacramento River remains just below 70°F.

Upstream from the mouth of the Feather, water temperatures in the Sacramento River are increasingly problematic. The hundred miles of river upstream from the mouth of the Feather to Hamilton City (RM 200) have a Central Valley Basin Plan upper temperature limit of 68°F in summer to protect the salmon during their run up the river in summer and fall. The only water temperature recorder is at Wilkins Slough, about mid-way in the reach, about 20 miles below Colusa (RM 143). Water temperature at Wilkins Slough has risen from 65°F to 72°F in the past week.

Summer water temperatures at Wilkins Slough vary with air temperatures, but are also determined in part by river flow. In the critically dry year last summer, water temperatures in July approached the lethal level for salmon of 80°F (Figure 1) under very low river flows (Figure 2). In below-normal year 2010, water temperatures were cooler (Figure 3) under higher river flows (Figure 4).

The flow at Wilkins Slough has increased over the past week from 3500 cfs to 5000 cfs, but the water temperature has continued to rise to 72°F with higher air temperatures. With even warmer air temperatures forecasted in the coming weeks, river flow should be increased to 6000 cfs or higher as in 2010 to maintain water temperature below 72°F. Temperatures above this level impede migration and stress adult salmon. A flow of 8000 cfs, as occurred in the summer of dry year 2012, would be more protective (Figures 5 and 6).

Figure 1. Water temperature at Wilkins Slough on the Sacramento River (RM 125) in June-July 2015, a critically dry year.

Figure 2. Sacramento River flow at Wilkins Slough in June-July 2015.

Figure 3. Water temperature at Wilkins Slough on the Sacramento River (RM 125) in June-July 2010, a below normal year.

Figure 4. Sacramento River flow at Wilkins Slough in June-July 2010.

Figure 5. Water temperature at Wilkins Slough on the Sacramento River (RM 125) in June-July 2010, a dry year.

Figure 5. Water temperature at Wilkins Slough on the Sacramento River (RM 125) in June-July 2012, a dry year.

Figure 6. Sacramento River flow at Wilkins Slough in June-July 2012.

June Update and Possible Solution to 2016 Fish Woes

Posted on June 21, 2016 by Tom Cannon

Over the past month I related water issues involving Delta and longfin smelt, striped bass, green and white sturgeon, and winter-run and spring-run salmon. All of these species need river flow and cooler water over the next several months. Shasta releases to the upper Sacramento River need to be cold, stable, and sufficient to sustain winter-run salmon eggs in the river near Redding and to sustain moderate flows and cooler water temperatures for 200 miles of river to protect sturgeon and other lifestages of salmon. Sufficient flows needs to pass through the Delta to keep the low salinity zone downstream of the Delta in the cool waters of eastern Suisun Bay, away from Delta exports.

Shasta releases are now 8000 cfs, with Bend Bridge water temperature near the Red Bluff target of 56°F. In June and July of drought years 2012 and 2013, releases were 11,000-14,000 cfs. However, concern over carryover storage and sustaining cold-water releases through summer has led to a more conservative management strategy in 2016. The cold-water pool in Shasta Reservoir is being rationed to make it through the summer. Flows will rise over the next six weeks to 9,000 or 10,000 cfs to satisfy irrigation demands in the upper river.

Flows in the lower Sacramento River at Wilkins Slough need to be greater than 5000 cfs in summer, if only to keep water temperature down closer to the Basin Plan’s 68°F. Flows are now 3000-4000 cfs, with water temperatures up to 75°F. In dry years 2012 and 2013, flows at Wilkins Slough were 6000-9000 cfs, and water temperatures were cooler, as some of Shasta’s storage was allocated for Delta export. This year’s management strategy to hold back Shasta releases will, if continued, keep both Wilkins Slough flows and Delta exports down.

Delta outflows need to be sustained near 10,000 cfs to keep the low salinity zone and X2 (2 ppt salinity) near Collinsville in eastern Suisun Bay. However, July outflow to the Bay required by water quality standards will be only about 8000 cfs. To help save the last of the two smelt species, 10,000 cfs would be far better.

A reasonable solution is apparent: raise Shasta releases through most of the summer by 2000 cfs to 10,000-12,000 cfs and require that the extra release be passed down the river to and through the Delta. While such a management strategy would benefit the fish, it would decrease Shasta storage by 120,000 acre-ft of water per month. At present, Shasta is 90% full at 4.1 million acre-feet (the cold-water pool volume is about 2.4 maf). At 12,000 cfs, the total Shasta release would rise to 600,000 acre-feet per month, which is about the current total release from Oroville (Feather River) and Folsom (American River) reservoirs. NMFS and USBR have determined that a 10,000 cfs Shasta cold-water release can be sustained through the summer, while a 12,000 cfs release could be problematic. Protests would no doubt come from water users who would want the extra 2000 cfs. But note that of the 20,000 cfs being released today from the three main Sacramento Valley reservoirs, only 8000 cfs is reaching the Bay.¹

This solution of raising total reservoir releases to 22,000-24,000 and Bay outflow to 10,000 cfs is reasonable to help the fish after four years of drought. In 2014-2015, water quality standards were drastically reduced, with catastrophic effects to fish. The continuing legacy of these catastrophic effects creates the urgency to do better in 2016.

If higher releases from Shasta become problematic for whatever reason, then some compromise should be achievable, noting that water deliveries of Shasta water are to be provided only after the needs of the fish are first considered, including conservation of Shasta’s cold-water pool through the summer and early fall (Water Rights Orders 90-05 and 92-02). Further, Central Valley water rights are provided via the Trinity River trans-basin diversion to Keswick Reservoir on the Sacramento River below Shasta Dam, but the Trinity supply is much in doubt because Trinity storage has failed to recover after the drought, unlike Shasta storage. A lack of Trinity supply this summer will further limit water available for irrigation in the Central Valley. Yet another constraint is whether the available storage in Oroville and Folsom reservoirs is able to satisfy Delta demands without compromising the needs of endangered fish in the Feather and American rivers.

Sorting out these conflicts and needs is the responsibility of the State Water Resources Control Board. The Board’s top priority should be the basic needs of the endangered salmon, sturgeon, and smelts of the Central Valley. At minimum, the Board should require the following conditions this summer:

Below Shasta – Stable flows of 9,000 to 10,000 cfs and 56°F average daily water temperatures near Red Bluff (Jellys Ferry or Bend Bridge).
Lower Sacramento River – minimum 5000 cfs at Wilkins Slough (RM 125 on the Sacramento River)
Delta Outflow – 9,000 cfs in July, 5,000 cfs in August, and 4,000 cfs in September.

A further complication is that South Delta export criteria allow an increase from 35% of inflow to 65% starting July 1. Exports in June are limited to 5000 cfs. In July, exports can be raised to 65% of inflow, but only if outflow is kept at 8000 cfs. Delta ag diversions are also near 4000 cfs. Thus July Delta inflow of 20,000 cfs or more (compared to the present inflow of 15,000 cfs) would be needed to allow 10,000 cfs of Delta export. ↩

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.