Summer 2016 Delta Salinity and Outflow Standards

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

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

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.

Are Delta Smelt Starving?

The Sacramento Bee reported on August 31, 2016 that Dr. Ted Sommer at the California Department of Water Resources says that Delta smelt are starving. Dr. Sommer related recent success in stimulating the north Delta food web (Figure 1) by increasing flow through the Yolo Bypass in July as part of the state’s new strategy to help Delta smelt. I had reported earlier on the experiment and the strategy.

While Dr. Sommer was not implying that just adding some fertilizer to the north Delta would save the smelt, he was deflecting discussion and treatment away from the overriding cause of the collapse of Delta smelt: lack of spring-through-fall outflow to the Bay.

During August of this year, the normal heavy hand of Delta exports again reached out to degrade the critical habitat of what few smelt are left (Figure 2). In summer, Delta smelt concentrate near X2, the area of the estuary where brackish water of about 2 ppt salinity occurs. Food concentrates at X2, as shown in Figures 3 and 4. Chlorophyll levels at X2 are an order of magnitude higher than at Rio Vista (Figure 1), where Dr. Sommer observed the increase in chlorophyll from the recent experiment.

X2 also has cooler water temperatures and higher turbidities preferred by smelt (Figures 5 and 6). It is at X2 where smelt are meant to be so they do not starve, do not get eaten, and do not die from high water temperatures. The problem is that X2 habitat readily degrades when summer outflow is low (4000 cfs) and exports are high (11,200 cfs). Under these conditions, low-salinity habitat and food (plankton) are siphoned off with each tide into False River, into Dutch Slough, and further upstream into the San Joaquin River channel (also shown in Figure 2).

Smelt did fine in summer 2011, the year with the last decent fall smelt index. X2 was much further downstream, and Delta outflows were high (15,000 cfs). If X2 stays out of the Delta, and smelt can get to X2 and stay there, they and their food supply will be far better off. This requires about8,000-10,000 cfs outflow in July and 6,000-8,000 cfs outflow in August. The present 4,000 cfs outflow index (real outflow, as opposed to the index, is closer to zero – see Figure 2), while exports are11,200 cfs just does not meet their needs.

Figure 1. Chlorophyll concentrations at Rio Vista in the north Delta July 23 to August 31, 2016.

Figure 1. Chlorophyll concentrations at Rio Vista in the north Delta July 23 to August 31, 2016.

Figure 2. Net Delta hydrology (flow in cfs) on August 25/26 during a spring tide. Net Delta outflow is near zero with positive net flow in the Sacramento channel (north) and negative net flows in the San Joaquin channel (south). Exports were near maximum at 11,200 cfs. The location of X2 (2 ppt salt) at high tide is shown as magenta line.

Figure 2. Net Delta hydrology (flow in cfs) on August 25/26 during a spring tide. Net Delta outflow is near zero with positive net flow in the Sacramento channel (north) and negative net flows in the San Joaquin channel (south). Exports were near maximum at 11,200 cfs. The location of X2 (2 ppt salt) at high tide is shown as magenta line.

Figure 3. Chlorophyll concentrations in summer 2016 at Blind Point in the lower San Joaquin channel (magenta line in Figure 2). Red circles denote periods when X2 moved upstream to Blind Point.

Figure 3. Chlorophyll concentrations in summer 2016 at Blind Point in the lower San Joaquin channel (magenta line in Figure 2). Red circles denote periods when X2 moved upstream to Blind Point.

Figure 4. Salinity in summer 2016 at Blind Point in the lower San Joaquin channel (magenta line in Figure 2). Red circles denote periods when X2 approached Blind Point.

Figure 4. Salinity in summer 2016 at Blind Point in the lower San Joaquin channel (magenta line in Figure 2). Red circles denote periods when X2 approached Blind Point.

Figure 5. Water temperature in summer 2016 at Blind Point in the lower San Joaquin channel (magenta line in Figure 2). Red circles denote periods when X2 approached Blind Point.

Figure 5. Water temperature in summer 2016 at Blind Point in the lower San Joaquin channel (magenta line in Figure 2). Red circles denote periods when X2 approached Blind Point.

Figure 6. Turbidity at Blind Point in the lower San Joaquin channel (magenta line in Figure 2). Red circles denote periods when X2 approached Blind Point.

Figure 6. Turbidity at Blind Point in the lower San Joaquin channel (magenta line in Figure 2). Red circles denote periods when X2 approached Blind Point.

Figure 7. Concentrations of Delta smelt in the Summer Townet Survey July 2011. Magenta line is location of X2.

Figure 7. Concentrations of Delta smelt in the Summer Townet Survey July 2011. Magenta line is location of X2.