Category Archives: Water Quality

Fundamental Needs of Central Valley Fishes – Part 1a: River Flows – First Pulse of Fall Rains

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In the coming months and years, regulatory processes involving water rights, water quality, and endangered species will determine the future of Central Valley fishes.

To protect and enhance these fish populations, these processes will need to address four fundamental needs:

  1. River Flows
  2. River Water Temperatures
  3. Delta Outflow, Salinity, and Water Temperature
  4. Valley Flood Bypasses

In this post, I summarize a portion of the issues relating to River Flows: Fall Rains. Part 1b will cover winter river flows.

River Flows – Fall Rains

In most years, the first substantial fall rainfall stimulates many important ecological processes such as salmon and smelt spawning runs and salmon and steelhead smolt migrations to the ocean.  Figure 1 below shows the effects of 2016’s late October rains,  and Figure 2 below shows the effects of 2015’s December rains, in the lower Sacramento River flows at Wilkins Slough near Yuba City below Colusa.  Most of these flow pulses came from storm runoff from un-dammed upper Sacramento Valley tributaries such as Cow, Cottonwood, and Battle Creeks.  Such flow pulses stimulate the migrations of young salmon toward the ocean.  Figure 3 below documents these migrations in the form of  rotary screw trap collections at Knights Landing in the lower Sacramento River.

Under current operations, flows from the major reservoirs are generally held to the minimum requirement in the fall season in order to increase reservoir storage (Figure 4).1  What is needed are flow pulses (spills) from the major Valley reservoirs to the major rivers below dams, to stimulate the migration of the juvenile salmon spawned immediately downstream of these dams.  Just downstream of Whiskeytown Reservoir on Clear Creek, Shasta and Keswick reservoirs on the upper Sacramento River, Oroville Reservoir on the Feather River, and Folsom and Nimbus reservoirs on the American River are vitally important salmon-producing reaches whose flow is completely controlled by the operation of the dams.  Water releases timed to the natural flow pulses would stimulate migration from these important salmon-producing reaches, providing even more flow and stimulus for young salmon from all the Valley rivers to pass successfully through the Delta and Bay to the ocean.

Meanwhile, downstream in the Delta, the CVP and SWP export facilities generally ramp up exports during the initial storm pulse (Figure 5 below shows an example from 2016).  Because of the importance of the initial storm pulse, the CVP and SWP should limit exports during the initial pulse, not only to help salmon get through the Delta and Bay, but also to minimize the diversion of young salmon to the south Delta.

Figure 1. Lower Sacramento River flow at Wilkins Slough in fall 2016.

Figure 1. Lower Sacramento River flow at Wilkins Slough in fall 2016.

Figure 2. Lower Sacramento River flow at Wilkins Slough in late fall 2015.

Figure 2. Lower Sacramento River flow at Wilkins Slough in late fall 2015.

Figure 3. Catch of juvenile salmon in Knights Landing rotary screw traps 2001-2004 vs. flow in lower Sacramento River at Wilkins Slough.

Figure 3. Catch of juvenile salmon in Knights Landing rotary screw traps 2001-2004 vs. flow in lower Sacramento River at Wilkins Slough.

Figure 4. Release of water from Shasta/Keswick to upper Sacramento River near Redding, fall 2016.

Figure 4. Release of water from Shasta/Keswick to upper Sacramento River near Redding, fall 2016.

Figure 5. Export of water from south Delta by State Water Project, fall 2016.

Figure 5. Export of water from south Delta by State Water Project, fall 2016.

  1. For additional discussion of the negative effects of this practice, see previous post. ↩

American River Salmon Hatchery Begins Taking Salmon

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California Department of Fish and Wildlife has announced that it opened the American River Nimbus Hatchery ladder on Nov 2.  At the same time, the feds have managed to cool down the river to allow salmon in the river to also begin spawning (Figure 1).  The Bureau of Reclamation cooled the river by opening lower level outlets of Folsom Dam for a portion of the day beginning in late October (Figures 2 and 3).  This allowed the release of  colder water from deep in the reservoir into the Nimbus regulating reservoir directly downstream of Folsom Reservoir.  There, the cold water mixed with warmer reservoir waters before discharge to the lower American River.

The real story here is that the feds had to wait until November to cool water both in the river, and in the Nimbus Fish Hatchery just downstream of Nimbus Dam.  The supply of cold water in Folsom Reservoir is limited this fall because of excessive releases of stored water to the Delta this past summer (see prior post).  The summer shrinkage of Folsom’s cold-water pool subjected the salmon that entered the lower American River in September and October to a month or more of stress from warm water.  That stress will likely reduce survival of pre-spawn and spawning salmon, diminish their success in spawning, and make many of eggs and embryos spawned in the river unviable.

Figure 1. Water temperature below Nimbus Dam on the lower American River near the Nimbus Hatchery Oct 4 – Nov 2, 2016. Red line denotes safe water temperature for holding and spawning salmon, and salmon egg survival.

Figure 1. Water temperature below Nimbus Dam on the lower American River near the Nimbus Hatchery Oct 4 – Nov 2, 2016. Red line denotes safe water temperature for holding and spawning salmon, and salmon egg survival.

Figure 2. Temperature of the water released from Folsom Dam Oct 21 – Nov 2, 2016. Red circles show the release of water from Folsom’s cold-water pool.

Figure 2. Temperature of the water released from Folsom Dam Oct 21 – Nov 2, 2016. Red circles show the release of water from Folsom’s cold-water pool.

Figure 3. Flow releases from Folsom Dam. Red circles depict flow releases of cold water from lower level outlet of dam Oct 21 – Nov 2, 2016.

Figure 3. Flow releases from Folsom Dam. Red circles depict flow releases of cold water from lower level outlet of dam Oct 21 – Nov 2, 2016.

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.