Category Archives: Water Quality

Scott River Chinook Crisis

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Klamblog1 recently reported that the Scott River Chinook salmon are again delayed from ascending the lower Scott from the Klamath River because of low water flow. This major Klamath tributary to the west of Mt. Shasta and Weed, CA that flows most winters with thousands of cubic feet per second (cfs) from rain and snow from the Trinity and Marble mountains has been flowing at less than 10 cfs this summer and fall. The salmon simply cannot migrate up this large, steep river with such low flow, especially in dry years when there is no snowmelt after June. The salmon simply wait for rain at the mouth of the Scott. Rains often come by December, just in time for California’s last viable run of Coho salmon, but too late for the Chinook.

As usual the blame is on irrigators in Scott Valley who draw down the water table with heavy groundwater pumping and surface water diversions in the summer for hay and pastures. The State Board did restrict most surface diversions this summer, but with little snowpack there was little streamflow to restrict. Scott Valley often has high groundwater, but with little snowpack recharge, less flood irrigation, and heavy pumping, groundwater seepage and ag returns to the river have virtually ceased, leading to the low flows.

Surprisingly, there is a solution that ranchers are willing to do – pump groundwater into the river in the fall after the summer irrigation season. There is more than enough pumping capacity and groundwater available. Ranchers only want payment for the electricity – a reasonably modest cost. In years like this we are talking about 8 to 10 weeks of a nominal amount of pumping and groundwater storage with a high likelihood that the groundwater used would be replaced/recharged this coming winter and spring.

The concept and proposal have fallen on deaf ears, and the ranchers have circled their wagons much like the salmon in the video link below. As the political fight over water goes on, we should take every opportunity like this one to save the salmon from extinction.

 

Save the Winter Run Salmon

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By now most everyone has seen the newspaper articles on the catastrophic decline in Winter Run Chinook salmon production in the Sacramento River below Shasta Reservoir in 2015. The number of Winter Run juveniles passing downstream past Red Bluff is down substantially from last year, when the estimated survival rate was 5%.  Many blame the drought  – the fourth year of drought.  I have blamed poor water management and the weakening of water quality standards prescribed to protect the salmon (see previous posts).

It is now time for extreme actions to save these fish.  This coming year’s winter adult run will be made up primarily of the 2013 spawn, with some from 2012.  These spawns were marginally successful and could produce enough spawners next summer to help fix this debacle.

The responsible agencies plan to take more eggs and increase smolt production at the Livingston Stone Hatchery near Redding.  They also plan to truck these hatchery smolts to the Bay to maximize their survival.  They will likely severely limit commercial and recreational fisheries that may harvest Winter Run.  They plan to again start raising a rescue population in captivity to ensure they have some fish in the future to draw on for recovery.  A new drought plan will again address how flows and water temperatures will be managed below Shasta.  The State Board may resist weakening Sacramento River and Delta water quality standards designed to protect Winter Run, unlike what they did in the last two years.  All of these actions together will indeed help Winter Run from further decline, but it will not be enough even if the El Niño brings abundant rain and snow.

What else?  The answer to that question should be everything that is reasonably possible to increase production and survival.  Here are some suggestions:

  1. Do not weaken Sacramento River and Delta water quality standards that protect Winter Run. (This alone would have averted the catastrophes below Shasta the past two years.)
  2. Minimize warm water inputs to the Sacramento River in summer from the Trinity River to keep Sacramento River temperatures lower and save Shasta’s cold-water pool.
  3. Alter peaking hydropower management and system infrastructure in Shasta-Trinity CVP system to improve water temperatures in the Sacramento River and the conservation of reservoir cold-water pools.
  4. Further limit Shasta-Trinity reservoir releases to water contractors to conserve cold-water pools and maintain flow requirements for salmon.
  5. Enhance natural winter and spring flow pulses from tributaries below Shasta with flow releases from Shasta to increase survival of emigrating wild juvenile salmon migrating downstream in the Sacramento River, to and through the Delta, and to and through the Bay to the ocean.
  6. Conduct an aggressive rescue program of adult Winter Run that migrate into Sacramento Valley bypasses only to be blocked below overflow weirs, or that migrate into dead-end basins, or that stray into other tributaries including Battle Creek, Feather River, and American River salmon hatcheries.
  7. Capture wild juvenile Winter Run in an enhanced trapping program at fish screen bypasses, screw traps, and other techniques in the Sacramento River in fall and winter migration period, and transport these juveniles to the Bay to avoid lower river and Delta sources of mortality.
  8. Modify Delta operations to maximize juvenile Winter Run survival through the Delta. This may involve further changes to Delta Cross Channel operations and Delta export schedules, as well as Delta inflow and outflow.
  9. Maximize egg taking and rearing capacity in hatchery system.
  10. Barge wild and hatchery young from the Sacramento River through the Delta for release in the Bay to avoid future straying problems associated with trucking fish.
  11. Raise juvenile hatchery salmon in floodplain habitats in winter in the Sacramento Valley (e.g., Sutter and Yolo Bypasses).
  12. Conduct egg injection or fry releases in appropriate locations in Battle Creek to jumpstart its prescribed new population; this can be managed at the Battle Creek hatchery.
  13. Develop and implement an emergency comprehensive plan with appropriate agencies with the necessary authority to carry out these actions. Include stakeholders in the plan development and review process.  Obtain necessary funding from available sources.

Sturgeon and the Drought

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The State Water Board’s weakening of the water temperature standards in the Sacramento River below Shasta at the request of Reclamation and concurrence by NMFS this late spring and early summer has likely led to excessive take during this spawning season of listed Green Sturgeon, increasing their risk of their extinction. Lower flows and higher temperatures in the Sacramento River’s Green Sturgeon spawning reach from Anderson (RM 280) to Hamilton City (RM 200) has likely resulted in a substantial mortality of eggs and larval Green Sturgeon, as well as White Sturgeon, during and following their May-June spawning season.

Water temperatures below Red Bluff (RM 240) exceeded the upper thermal optimum for Green Sturgeon embryos (17-18°C, 62-65°F1) from late spring to early summer 2015 (Figure 1), but rarely in 2012, the first year of the present drought (Figure 2), when standards were not weakened. Water temperatures exceeded 62°F nearly to Anderson at times this summer (Balls Ferry and Jelly’s Ferry). Approximately half the spawning reach has been severely degraded by warm water from weakened standards (Figure 3). Lower flows and higher water temperatures have likely led to earlier spawning and more concentrated spawning in the upper end of the spawning reach. The river below Hamilton City, where eggs and fry drift and many young rear, is degraded with high water temperature even above 100% lethal levels (23°C, 73°°F) at Wilkins Slough (RM 120) (Figure 4). In 2012, when standards were not weakened, conditions at Wilkins Slough were much better and near optimum (Figure 5). However, even in 2012 (the first year of the present drought cycle) Green Sturgeon tended to spawn further upstream in the spawning reach than in previous years2 because of lower river flows and/or higher water temperatures.

What applies to Green Sturgeon also applies to the non-listed White Sturgeon, whose spawning and rearing requirements, timing, and locations are similar to those of the Green Sturgeon3. Concerns for the White Sturgeon are ever increasing4. The risks extend to adult White Sturgeon, which have undergone a die-off in the Columbia River under similar circumstances5.

Figure 1

Figure 1. Water temperatures at Red Bluff on Sacramento River late spring and early summer 2015. (Source: CDEC)

figure 2

Figure 2. Water temperatures at Red Bluff on Sacramento River late spring and early summer 2012. (Source: CDEC)

Figure 3

Figure 3. Green Sturgeon spawning reach in the Sacramento River (green highlight). Reach degraded by high water temperature in 2015 (red highlight).

Figure 4

Figure 4. Water temperatures at Wilkins Slough (RM 120) on Sacramento River late spring and early summer 2015. (Source: USGS)

Figure 5

Figure 5. Water temperatures at Wilkins Slough (RM 120) on Sacramento River late spring and early summer 2012. (Source: USGS)

  1. “Water temperature for spawning and egg incubation is near optimal (15oC/ 59oF)) from RBDD upriver during the spawning season. Below RBDD, water quality, in terms of water temperature, gradually degrades and eventually exceeds the thermal tolerance level for egg incubation, when egg hatching success decreases and malformations in embryos increase above 17 oC/62 oF, at Hamilton City”. (NMFS OCAP Biological Opinion p276) ↩
  2. William R. Poytress, Joshua J. Gruber, Joel P. Van Eenennaam & Mark Gard (2015) Spatial and Temporal Distribution of Spawning Events and Habitat Characteristics of Sacramento River Green Sturgeon, Transactions of the American Fisheries Society, 144:6, 1129-1142, DOI: 10.1080/00028487.2015.1069213 ↩
  3. White Sturgeon generally spawn lower in the river than Green Sturgeon. ↩
  4. http://www.scout.com/outdoors/fish-sniffer/story/1563429-ca-dfw-considers-slashing-sturgeon-fishing
    https://cdfgnews.wordpress.com/2015/08/11/responsible-angling-practices-help-conserve-sturgeon-populations/
    ↩
  5. http://www.cbbulletin.com/434540.aspx ↩

False River Barrier 2015

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This summer’s placement of the False River Barrier in the central Delta has been touted for saving reservoir storage during this fourth year of drought.

Contra Costa Times quoted DWR on the recent removal of the False River Barrier: “The state also managed to reduce the volume of fresh water it released from reservoirs to add to the Delta, preserving the resource instead for the times that salmon need infusions of colder water to survive.” (Contra Costa Times 10/2/15)

DWR also posted: “The barrier helped limit the tidal push of saltwater from San Francisco Bay into the central Delta and minimized the amount of fresh water that had to be released from upstream reservoirs to repel saltwater.”1

A DWR news release stated: “The barrier was an essential part of DWR’s strategy to maintain good water quality in the Delta and preserve water in upstream reservoirs to help keep young salmon cool enough to stay alive downstream of dams….The water users in the interior of the Delta, including many farmers and residents there, would have experienced much higher salinity without it… Monitoring at various stations in the Delta showed that the barrier indeed helped improve water quality in the central and south Delta.”2

Question 1. Did the False River Barrier save reservoir water by reducing release requirements?

A. Shasta – the answer is no, Shasta retained its prescribed releases all summer. There was thus no benefit of False River Barrier in retaining Shasta’s cold-water pool.
B. Trinity – no, it too contributed only to the fixed release to Sacramento River.
C. Oroville – releases to Feather River were relatively high much of the summer contributing substantially to Delta inflow.
D. Folsom – Releases to American River were relatively high all summer contributing substantially to Delta inflow, although depleting the reservoir’s overall storage and cold water pool.
E. New Melones – Stanislaus and San Joaquin flows were minimum all summer.

The overall answer is that slightly less Oroville and Folsom releases may have been needed with the False River Barrier; whether releases were lower or not is difficult to determine

Question 2. Was less freshwater outflow to the Bay required because of the False River Barrier?

No, outflow standards were prescribed by State Board and for the most part were met.

Question 3. Was less freshwater inflow needed to maintain the salinity standards at Threemile Slough, Jersey Point, and South Delta?

Threemile Slough was the controlling compliance point this summer, at times requiring increased Delta inflow and closure of the Delta Cross Channel for compliance. The False River Barrier likely increased the effectives of these measures to lower Threemile salinity.

Question 4. Did False River Barrier result in lower salinity in Central and South Delta?

No, salinities were higher than either 2013 or 2014.

Question 5. Was Franks Tract salinity lower because of the False River Barrier?

No, because salinity entered via the lower San Joaquin from San Andreas Landing via the mouth of Old River, as both these sites had higher salinity than in 2013 or 2014. The lower San Joaquin from Jersey Point to Prisoners Point thus suffered higher salinities in 2015 to meet South Delta export demands without False River inputs.

Question 7. Were South Delta exports higher than would have been possible without the False River Barrier?

Yes, because a higher proportion of freshwater inflow from the Sacramento River via the Delta Cross Channel and Georgiana Slough could be exported with False River closed.

Conclusion:

The Department of Water Resources’ assertion in the news article that salmon benefitted from the False River Barrier is unfounded. There were no measurable savings to reservoir storage or cold water pools essential to salmon.

Salinity found another path into Franks Tract via the mouth of Old River, but to the detriment of upstream movement of the Low Salinity Zone in the lower San Joaquin River. South Delta exports were able to take a higher portion of the freshwater inflow to the Delta from the Sacramento River because of the False River Barrier. Higher South Delta salinities in 2015 demonstrated a willingness to accept higher salinities in exports with the False River Barrier in place or simply an extreme demand for some summer export. Salinities dropped sharply in September with higher freshwater inflows (and outflows) to accommodate South Delta export and water transfers. The transfers were possible as water demands from the Sacramento Valley and Delta sharply declined, and water was sold for transfer south of the Delta. The False River Barrier likely helped facilitate the across-Delta transfers, which declined after the False River Barrier was removed at the end of September.

State Water Projects south Delta exports at Clifton Court Forebay summer 2015

State Water Projects south Delta exports at Clifton Court Forebay summer 2015.

Central Valley Project south Delta exports at Tracy Pumping Plant summer 2015.

Central Valley Project south Delta exports at Tracy Pumping Plant summer 2015.

Environmental Water and the Cantankerous Bay-Delta

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Challenges Facing the Sacramento-San Joaquin Delta

Repelling Salinity

One often hears during this present four-year drought about all the water being “wasted” on the Bay-Delta environmental water. The fact is that, other than the millions of acre-feet going to water supply diversions, most of the so-called “environmental water” goes to repel salinity so that water entering the Delta may be exported. Very little water is going directly to help the Bay-Delta estuary ecosystem. Last winter and spring, storm water not captured by reservoirs did reach the Delta in modest pulses. These pulses were protected to some extent by restrictions on exports required by biological opinions and state water quality standards. Other than these environmental protections that served during these short pulses to help young salmon pass through the Delta, there has been little “environmental” water for the rivers or Bay-Delta since 2012. Outflow requirements, salinity standards, and export restrictions were weakened or simply not enforced during the past three years.

All the reservoir releases were designated for water supply diversions. Over 1 MAF of Shasta releases went to Valley water contractors. Over 2 MAF of reservoir releases went to the South Delta state and federal exports. Over 1 MAF went to Delta farmers. About 1 MAF went to repelling salinity to make the 3 MAF of Delta diversions possible.

Some excellent information and discussion was presented on the topic of repelling salinity this year. One of my favorites is a YouTube video (https://youtu.be/9M4XcLQkqEM ) that shows how salt attacks the Delta during a typical lunar tidal period. Another is an article in the San Francisco Estuary Partnership newsletter on the Delta salt-field (http://www.sfestuary.org/salt-field/ ). A great tool for viewing the dynamic Delta salinity field can be found at: http://www.baydeltalive.com/salinity.

The newsletter article recalls a recent ad hoc meeting of Delta scientists, modelers, and managers trying to come up with drought mitigation strategies that “wouldn’t burn so much water to keep the salt field at bay”. In other words, they were looking for ways to export more of the reservoir water entering the Delta. Those at the meeting discussed cutting exports, opening the Delta Cross Channel gates, and ceasing operation of the Suisun Marsh salinity control gates. Other than the obvious benefit of reducing exports (contrary to the meeting’s purpose), the other two options were to eliminate key environmental protections. Jon Burau (USGS) was quoted as saying: “these would be the quickest, least expensive things we could do to save water that would also have the least impact on the ecosystem.” The cross channel gate closures are required in biological opinions and water quality standards in winter-spring to keep endangered Sacramento River salmon and steelhead from entering the Central and South Delta and being lost. The Marsh salinity gates are critical in the management of the Marsh wetland ecosystem and maintenance of Montezuma Slough’s critical habitat for the two listed smelt species.

In 2015, Department of Water Resources (DWR) added a salinity barrier to the existing array of Delta barriers: the False River Barrier was eventually installed to keep salt from entering the interior Delta through Franks Tract. At the behest of DWR and the Bureau of Reclamation, the State Water Resources Control Board weakened the salinity standard by moving the compliance point five miles from Emmaton to Threemile Slough. The Board also weakened the Delta outflow standards that keep the Low Salinity Zone out of the Delta, “saving” up to several thousand cfs. In a completely unprecedented action this summer, Reclamation actually closed the Delta Cross Channel to keep salt from the salinity control site at Threemile Slough near Rio Vista. This action was possible because of the presence of the False River Barrier. The goal for managing the Delta this year was simply to keep the salt level of South Delta exports at or below the 800 EC level.

With the Delta “scientists, modelers, and managers” who manage the Delta water system thinking in terms of water “burn”, four independent Delta ecosystem scientists recently wrote a paper on the “Challenges Facing The Sacramento-San Joaquin Delta: Complex, Chaotic, or Simply Cantankerous? “1. They describe the “Delta Problem” in terms of “wicked problems” – “Such problems can’t be ignored, defy straight-forward characterization, and have no simple solutions. Yet they must be actively managed to maximize beneficial and minimize adverse outcomes”. (From ‘DeltaChallenges-v13,’ page 6). With such divergent philosophies managing the Delta, it is no wonder the Delta Problem is perceived as “wicked”. The four scientists further conclude that “opportunities exist to conserve and restore aspects of the native system and to structure the rest of the Delta to make it more hospitable to native species. Realizing those opportunities without jeopardizing water supply is the ultimate challenge in managing the Delta.” (From ‘DeltaChallenges-v13’, page 28).

It appears that one side is intent on minimizing water “burn”, while the other deals with the resulting “wicked problems” that come from the focus on water supply.

The Solution

It is a not “wicked problem.” It is a matter of switching the focus of Delta management away from minimizing “water burn” to maximizing ecosystem health and protecting endangered fish with the water available. The Valley river and Delta water quality standards for dry and critical water years were developed to provide minimal protections. Step 1 should be to maintain and enforce these standards for streamflow, water temperature, and Delta outflow and salinity. These standards could have been retained in each of the past three years with just 10% of the 4+ MAF of reservoir water delivered for water supply. If there are really “co-equal” goals, then the ecosystem getting 10% instead of near zero is a bargain. If we want to begin recovery of the Bay-Delta ecosystem from its present near-death state, we should be considering a much larger percentage of dry year water supply to meet the “co-equal” goal.

Climate change is putting a real hurt on California water supply that is very real and likely long lasting. Hard decisions and massive investments will be needed to adjust to a more reliable water supply system. However, the ecosystems and native species of California rivers, the Delta, and the Bay should not be sacrificed in the short term for the sake of water supply. The threatened and endangered fish depending on our California ecosystems cannot wait. They need the water now to survive.