Author Archives: Tom Cannon

Delta Smelt Summer 2016 Update

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Past summer surveys in the Cache Slough, Liberty Island, and Deepwater Ship Channel areas of the northern Delta frequently collected Delta smelt. Some documents even referred to this area as the last refuge of Delta smelt.

“The southern end of the Yolo Bypass, including Liberty Island (Table 9-2), Cache Slough, and the DWSC are known to support Delta Smelt spawning and rearing (Bennett 2005) (Grimaldo et al. 2004). The USFWS found Delta Smelt in shallow water habitats within Liberty Island using a variety of fish sampling techniques (Figure 9-1). Delta Smelt catch and gonadal staging from fish collected from the Spring Kodiak Trawl (SKT) surveys also indicate that the DWSC is an important spawning location in the Delta (Figure 9-2). Additionally, a non-migratory contingent has been recently observed to remain in freshwater and carry out their entire lifecycle in the tidal freshwater region of the CSC, which offers cool, turbid habitat and abundant prey (Sommer et al. 2011). DWR 2015 1

Surveys picked up some Delta smelt in the northern Delta even in the 2012-2015 drought years. In fact, most of the few smelt detected in those years came from this area.

However, the 2016 Summer Townet surveys caught no smelt in the northern Delta’s Cache Slough area at all. The extreme water temperature conditions present in 2012-2015 (August water temperatures in the 23-26°C range, near lethal to smelt) occurred again this summer (see chart below).

One Delta smelt was caught this summer downstream of the Delta, in Grizzly Bay at the mouth of Montezuma Slough.  There is at least one Delta smelt left.  Hopefully, the Fall Trawl Survey will collect a few more.

Water temperature (°C) in lower Yolo Bypass Tule Canal (green) and adjacent Deepwater Ship Channel (blue) in July 2016. (USGS data)

Water temperature (°C) in lower Yolo Bypass Tule Canal (green) and adjacent Deepwater Ship Channel (blue) in July 2016. (USGS data)

  1.  Draft FRP Cache Slough Complex Conservation Assessment, p. 9-2, http://www.water.ca.gov/environmentalservices/cache_slough_assessment.cfm  ↩

Shasta Success?

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It would appear that this year’s management of Shasta Reservoir’s cold-water pool by federal and state agencies responsible for Sacramento River salmon has been at least partially successful in meeting objectives.  Unlike the last two drought years (2014 and 2015), adequate cold-water storage and releases from Shasta were sustained through summer 2016 to protect winter-run salmon eggs and embryos in gravel beds.  Water temperatures were generally kept within safe margins, and water levels were sustained to limit stranding of eggs and embryos.  It remains to be determined whether spawning and rearing conditions were adequate to reach target survival estimates for winter-run salmon smolts.

Shasta Cold-Water Pool

Operation of the lower gates of Shasta Dam’s Temperature Control Device (TCD) allowed access of Shasta Reservoir’s deeper colder water through October (Figure 1).  The temperature of the water released from the dam has been sustained at an average 52°F in September and October.  In September and October of 2014 and 2015 averages were 57/61°F and 54/57°F, respectively.

Water Temperature

On June 17, the control point for 2016 Sacramento River water temperatures was set at 56°F at Balls Ferry (25 miles below Keswick Dam near Redding).  Normally the regular control point is at Bend Bridge (41 miles below Keswick) as prescribed by NMFS and the State Water Board, but the change was allowed to conserve Shasta’s cold-water pool.  Water temperatures at Bend Bridge were above 56°F for most of the April-August period, even exceeding the safe adult salmon holding and spawning level of 59°F from mid-April through early June (Figure 2).  Although temperatures in 2016 exceeded objectives, they showed a marked improvement over summer 2014 (Figure 3), when depletion of the cold-water pool led to poor survival of the 2014 spawn.

Streamflow and Water Level changes

Streamflow and water level changes in 2014 led to stranding of salmon redds in 2014 (Figure 4).  Water level dropped 3 feet over the summer in 2014, including nearly 2 feet in August when most of the winter run eggs and embryos were still in the redds.  In contrast, water levels in 2016 changed little until September when levels dropped only 1.5 feet (Figure 5).  Most winter run salmon fry leave the redds by early October.

Figure 1. Latest operation of TCD.

Figure 1. Latest operation of TCD.

Figure 2. Water temperature at Bend Bridge in 2016. Yellow is safe level for adult holding and spawning. Red is normal target prescribed by NMFS and State Board.

Figure 2. Water temperature at Bend Bridge in 2016. Yellow is safe level for adult holding and spawning. Red is normal target prescribed by NMFS and State Board.

Figure 3. Water temperature at Bend Bridge in 2014. Yellow line is safe level for adult holding and spawning. Red is normal target prescribed by NMFS and State Board.

Figure 3. Water temperature at Bend Bridge in 2014. Yellow line is safe level for adult holding and spawning. Red is normal target prescribed by NMFS and State Board.

Figure 4. Stranded salmon redd in early fall 2014 after Shasta releases were curtailed when cold-water pool was depleted. (CDFW photo)

Figure 4. Stranded salmon redd in early fall 2014 after Shasta releases were curtailed when cold-water pool was depleted. (CDFW photo)

Figure 5. Water level at Bend Bridge in summer 2014.

Figure 5. Water level at Bend Bridge in summer 2014.

Figure 6. Water level at Bend Bridge in summer 2016.

Figure 6. Water level at Bend Bridge in summer 2016.

Summer 2016 Delta Salinity and Outflow Standards

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The present water quality standards for the Delta were established by the State Water Resources Control Board in 1995. The standards govern how the Delta water projects operate and indirectly control much of the Central Valley’s water management. The standards also have a substantial influence on the ecosystem health of river, the Delta, and the Bay . These standards have been under review for a decade and are badly in need of update and revision. These standards have been responsible for the decline of Central Valley native fishes, including the listing of six under state and federal endangered species acts.

In this post, I discuss the Delta standards relative to performance in summer 2016, the first near normal water year (at least for the Sacramento River watershed) after four years of drought.

The summer Delta standards govern Delta salinity, Delta outflow, Sacramento River flow at Rio Vista, and south Delta export limits. Of the four, salinity and outflow governed the Delta in summer 2016, with river flow and exports (percent of inflow) well within prescribed limits.

The salinity and outflow standards are monthly average limits (objectives). Monthly average standards of salinity are prescribed as electrical conductivity at Emmaton and Jersey Point in the west Delta (Figure 1), as well as other locations in the interior and south Delta.

The problem is that these standards are specifically designed to protect Delta agriculture and export water quality, not Delta ecology or its native fishes. That specific deficiency is what caused federal biological opinions to add restrictions to limit south Delta exports; however, none of these applied in summer 2016. Although the agricultural standards do provide some ecological protection, the specific hydrology shown in Figure 1 results in brackish water being drawn into the central and south Delta, which degrades the low salinity zone that is so critical to the Bay-Delta native fishes.

Figure 1. Western Delta salinity and flow monitoring stations. Blue arrow denotes primary source of fresh water input to Delta from the Sacramento River. Red arrows indicate net negative flows from west Delta toward south Delta export pumps in summer 2016. Under these conditions Jersey Point salinity tends to be controlling.

Figure 1. Western Delta salinity and flow monitoring stations. Blue arrow denotes primary source of fresh water input to Delta from the Sacramento River. Red arrows indicate net negative flows from west Delta toward south Delta export pumps in summer 2016. Under these conditions Jersey Point salinity tends to be controlling.

Delta Inflow

Approximately 4 million acre-feet (maf) of water entered the Delta from the Sacramento River in summer 2016, primarily from reservoir releases to satisfy agricultural demands and meet salinity/outflow standards. The 4 maf of Sacramento River inflow to the Delta represented approximately 90% of total Delta inflow. The remainder came from limited San Joaquin flow. and other sources.

Figure 2. Delta inflow from the Sacramento River in summer 2016.

Figure 2. Delta inflow from the Sacramento River in summer 2016.

Delta Outflow and Diversions

Of the approximately 4.4 maf of total Delta inflow in summer 2016 (Figure 3), only 1.8 maf (40%) reached the Bay. Total exports and diversions from the Delta were 2.6 maf (60% of total inflow). Delta outflow standards controlled until mid-July when salinity standards took control. The additional outflow for salinity control above that necessary to meet outflow standards was provided primarily by reducing south Delta exports by approximately 300,000 acre-ft because of limited available upstream reservoir storage.

Figure 3. Delta outflow in summer 2016. Red lines denote Delta outflow standards for a Below Normal water year. Higher outflows than prescribed after mid-July were required to meet salinity standards.

Figure 3. Delta outflow in summer 2016. Red lines denote Delta outflow standards for a Below Normal water year. Higher outflows than prescribed after mid-July were required to meet salinity standards.

Salinity

Salinity standards took control in July (Figure 4) as Delta outflow failed to keep brackish water from the Bay from encroaching up the San Joaquin channel to Jersey Point. After mid-August salinity standards for the south Delta (700-1000 EC limits) became controlling (Figure 5).

The Problem and Solution

Too much salt is allowed into the interior Delta in summer, resulting in the degradation of water quality of diversions/exports and of the low salinity zone habitat of native estuarine fishes, including Delta smelt.

The solution is to extend the early summer 450 EC standard at Jersey Point (Figure 4) through the summer in abundant water years where high exports are planned from the south Delta. In low water supply years when exports are curtailed due to limited reservoir storage, a less stringent standard can be applied. In addition, in drier years, barriers can be placed on False River and Dutch Slough to limit movement of brackish water (and low-salinity-zone fish and their food supply) into the interior Delta.

Figure 4. Salinity (EC) at Jersey Point in the San Joaquin channel of the west Delta in summer 2016. Red lines denote salinity standards applicable at Jersey Point in summer 2016.

Figure 4. Salinity (EC) at Jersey Point in the San Joaquin channel of the west Delta in summer 2016. Red lines denote salinity standards applicable at Jersey Point in summer 2016.

Figure 5. Salinity (EC) in Old River in south Delta in summer 2016. Red lines denote 30-day running average salinity standards applicable to south Delta.

Figure 5. Salinity (EC) in Old River in south Delta in summer 2016. Red lines denote 30-day running average salinity standards applicable to south Delta.

American River Salmon and Steelhead – Update

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In a September post I opined about the state of the American River salmon and steelhead.  I am more inclined now to scream.  This beautiful river running through the state’s capital city, Sacramento, one of the Central Valley’s top three producers of salmon and steelhead, is now the most abused.  Water temperatures and flows have reached critical limits  because of high summer releases from Folsom Reservoir, leaving this year’s salmon run in the lower American River in jeopardy.

After nearly filling this past spring, Folsom Reservoir was drained of an unprecedented 550,000 acre-ft of water (and most of its cold-water pool) over the summer (Figure 1) in support of cities and farms in central and southern California.  Fall flows from Folsom Lake to the 20 miles of the lower American River have been cut to drought levels (Figure 2) to conserve what minimal storage is left and to have some cool water for late fall salmon spawning.

The lower American River is now host to tens of thousands of adult Chinook salmon that have migrated into the river to spawn.  These salmon are now “holding” for their eggs to mature and for water temperature to fall below 60°F so that their spawned eggs can survive.  Scientific research has led the National Marine Fisheries Service, the Environmental Protection Agency, the California Department of Fish and Wildlife, and the State Water Resources Control Board to recommend “holding” water temperature be less than 60°F to ensure the health of the holding, pre-spawn salmon and the viability of their eggs.

At a time when nearly all the Central Valley spawning rivers are near 60°F or below, the lower American remains warmer (Figure 3), with daily average water temperatures of 65°F.

While fishing the lower American River on October 12, an adult female salmon swam up to me “gasping” for air.  Other than a raw lamprey scar, she appeared healthy.  I tried to revive her by holding her steady in a slight current, but she eventually died.  It took less than an hour for the carcass to be covered by silt and become unrecognizable.  I wondered how many more like her were on the bottom of the river.

I can only assume that fisheries agencies are desperately trying to manage the river to save as many salmon as possible given the warm, low water levels in Folsom Lake and the limited options that now remain available to them.  The main problem is this past summer’s draining of Folsom’s cold-water pool.  In future years, the Bureau of Reclamation and the fisheries agencies need to fully implement the requirements of the CVP/SWP biological opinions  as copied verbatim in my September post, linked above.

Figure 1. Folsom Lake storage in acre-ft in 2016. Maximum is 975,000 acre-ft. (Note: flood control limits in spring often keep the reservoir from filling.)

Figure 1. Folsom Lake storage in acre-ft in 2016. Maximum is 975,000 acre-ft. (Note: flood control limits in spring often keep the reservoir from filling.)

Figure 2. Flows from Folsom Lake to lower American River in 2016. Note the average of about 5000 cfs per day (10,000 acre-ft per day) released from early May to mid-August (roughly 1 million acre-ft from storage and reservoir inflow).

Figure 2. Flows from Folsom Lake to lower American River in 2016. Note the average of about 5000 cfs per day (10,000 acre-ft per day) released from early May to mid-August (roughly 1 million acre-ft from storage and reservoir inflow).

Figure 3. Summer to early fall water temperatures in the lower American River in 2016. Yellow line is target maximum-allowed standard. Red line is recommended maximum-allowed holding temperature limit for adult Chinook salmon.

Figure 3. Summer to early fall water temperatures in the lower American River in 2016. Yellow line is target maximum-allowed standard. Red line is recommended maximum-allowed holding temperature limit for adult Chinook salmon.

2015 Winter-Run Salmon Progress Report – Lessons Learned and Not Learned

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The Sacramento River Temperature Task Group’s report on water year 20151 released at the end of last year prematurely proclaimed successful operations for 2015 under its Temperature Control Plan (TCP). If the Group had waited a few more months, it would have reported utter failure, with the poorest survival and production of winter-run salmon yet recorded.2 Below, I excerpt from the Report, and offer some observations.

In summary, water year 2015 has been one of the driest years in decades and it followed three consecutive dry years throughout the state. Shasta Reservoir was projected to have end of year storage of 1.1 MAF in the May 90% forecast. Due to such low storage in Shasta Reservoir, Reclamation utilized Trinity River water to conserve Shasta Reservoir storage. The amount of water brought over from Trinity River through the Spring Creek Tunnel into Keswick Reservoir was a great benefit to the temperature operations on the Sacramento River. In all, Reclamation achieved meeting the TCP at Clear Creek (see Chart 1) of 57°F not to exceed 58°F through October 1, 2015, as indicated in the Temperature Management Plan, when 90% of the redds were emerging.

Comment: The Trinity water brought into Keswick Reservoir was 58-59°F, warmer than even the downstream criteria, resulting in more of the Shasta cold-water pool being used to cool it. The problem was recognized by the parties, as it resulted in demands to replace the existing Whiskeytown temperature curtain to cool the Trinity water before it was released into Keswick Reservoir. Achieving the 2015 goal of not exceeding 58°F turned out ineffective as well. Less than normal amounts of Trinity water have been brought into Keswick so far in 2016.

Despite the SRTTG best projection and modeling efforts to manage Sacramento River water temperature for winter-run spawning and egg incubation in water year (WY) 2014, winter-run brood year (BY) 2014 was considered a year class failure. One hundred percent of BY 2014 redds were exposed to temps above 56°F daily average temperature (DAT) at the Sacramento River above Clear Creek California Data Exchange Center monitoring station temperature compliance point (CCR) at some time period during WY 2014. Of significant concern were those eggs, alevin, and fry exposed to the elevated DAT above 56°F (and as high as 62.3°F) throughout September and October when the cold water pool out of Shasta Reservoir was depleted.

Comment: So the Task Group met the monthly average but allowed the daily average temperature to exceed 58°F in summer 2015 (Charts 2 and 3). The Report suggests improvement compared to 2014 conditions, but 2015 was also above 56°F. On 10% of the days in summer 2015, hourly water temperature exceeded 60°F at the CCR gage at Bonnyview Bridge in Redding during warm afternoons. On 60% of the days, water temperature reached or exceeded 59°F, the tolerance limit for salmon eggs and embryos. 3

Temperature monitoring results of 70 loggers indicated slight variation and stratification in temperature between in-river, backwater, and deep pools, but in general all winter-run salmon eggs and alevins were exposed to poor water quality due to warm water temperatures.

Comment: If they knew this, why did they allow it?

The plan called for real-time operations that targeted 57° at the Clear Creek compliance location not to exceed 58°F with minimized flows. By targeting 57°F not to exceed 58°F, where the majority of the redds were above Hwy 44, we were able to extend the use of the cold water pool.

Comment: By targeting the Clear Creek compliance location, the Task Group pretty much assured that adult winter-run salmon would seek out cooler waters near Redding, essentially confining their spawning to the uppermost 10 miles of their historic 60 mile spawning reach. The Group extended the cold-water pool by creating low survival conditions in the spawning reach. Reclamation was able to bring in warmer Trinity water for water supply (at the expense of Shasta’s cold-water pool) and did not have to sacrifice hydropower or peaking hydropower using Shasta Dam’s warm-water bypass (an operation which most likely would have been required if the target had been the appropriate 56°F). Reclamation was also able to meet its water supply commitment of 75% allocation to the Sacramento River settlement contractors in the fourth year of drought. So far in 2016, Reclamation has met its commitment of 100% allocation to the settlement contractors.

Perhaps more perplexing is what was left out of the report: water temperature and flow conditions in the salmon-migration and sturgeon-spawning reach in over 100 miles of the Sacramento River below Red Bluff. There was no mention of the Basin Plan’s targets for this reach of the river where water temperatures were too high (>22°C, 72°F) to allow adult salmon migration, while creating lethal conditions (>20°C, 68°F) for juvenile sturgeon4 (Chart 4). There was a complete disregard for the winter-run salmon objective of 56°C at Red Bluff in the Basin Plan, Water Right Order 90-05, and the NMFS BO: all 150 days from May through September failed to meet the objective (Chart 5). So far in 2016, the objective has yet to be met, despite the fact that Shasta was nearly full at the beginning of May.

Hopefully, the Winter Run 2016 report will be more comprehensive and complete than the Report for 2015. The 2016 Report should include not only the consequences for spawning habitat near Redding, but should also analyze the condition of rearing and migratory habitat below Redding through the fall and winter. The report should also cover consequences to the other salmon, including the ten million federal hatchery salmon smolts released near Redding.

Chart 1. Map of 60 miles spawning reach below Keswick Dam on Sacramento River. Various temperature compliance points are noted. The NMFS BO specifies Bend Bridge with relaxation allowed in drier years. In 2015 the compliance point was above Hwy 44 bridge. Clear Creek 58F DAT was the compliance point in spring 2016. Balls Ferry 56°F is present compliance point in summer 2016.

Chart 1. Map of 60 miles spawning reach below Keswick Dam on Sacramento River. Various temperature compliance points are noted. The NMFS BO specifies Bend Bridge with relaxation allowed in drier years. In 2015 the compliance point was above Hwy 44 bridge. Clear Creek 58F DAT was the compliance point in spring 2016. Balls Ferry 56°F is present compliance point in summer 2016.

Chart 2. Summary of 2015 spring-summer monthly average temperature at Clear Creek compliance point.

Chart 2. Summary of 2015 spring-summer monthly average temperature at Clear Creek compliance point.

Chart 3. Summer 2015 spring-summer water temperatures at compliance locations. Note the red line is one degree above the target 56°F they noted.

Chart 3. Summer 2015 spring-summer water temperatures at compliance locations. Note the red line is one degree above the target 56°F they noted.

Chart 4. Water temperature and river flow at Wilkins Slough at RM 125 on the Sacramento River May-September 2015. Historical average flow shown by green triangles.

Chart 4. Water temperature and river flow at Wilkins Slough at RM 125 on the Sacramento River May-September 2015. Historical average flow shown by green triangles.

Chart 5. All 150 days from May through September were higher than the 56°F Basin Plan objective for Red Bluff.

Chart 5. All 150 days from May through September were higher than the 56°F Basin Plan objective for Red Bluff.