Category Archives: Bay-Delta

More on Delta Smelt Tidal Surfing

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The last post about risk to Delta smelt was on January 9. Adult smelt migrate into the Delta from the Bay in winter to spawn. They take advantage of the flood tide to move upstream. However, with flood flows as high as 100,000 cfs entering the north Delta from the Sacramento River, the Yolo Bypass, and Georgiana Slough in mid- to late January 2017, there are no flood tides to ride into the north Delta spawning areas.

The only option for the adult smelt is thus to ride the incoming tide up the San Joaquin River into the central and south Delta (Figure 1). South Delta export pumping is currently at 14,000 cfs, near maximum capacity, using four rarely used auxiliary pumps. This pumping increases the pull of the incoming tide, reducing the effect of the inflow from the San Joaquin, Calaveras, Mokelumne, and Cosumnes rivers. While Delta inflow from these rivers is relatively high (Figures 2-5), it does not offset the influence of the incoming tide as does the inflow from the Sacramento.

Net tidal flows in lower Old and Middle Rivers (OMR flows) remain at the allowed limit of -5000 cfs, consistent with the smelt Biological Opinion. Several adult Delta smelt were salvaged at the export facilities in mid-January. 1 This scenario is considered a “high risk” to Delta smelt by the Smelt Working Group, because of the continuing risk that the pumps will draw or attract adult smelt into the central Delta and subsequently into the south Delta.

Under lower San Joaquin River flows, the maximum allowed export pumping is 11,400 cfs. High San Joaquin River inflow allows exports of 14,000 cfs that do not generate OMR flows more negative than -5000 cfs. The theoretical benefit of high San Joaquin River flows is that it should keep flow into the central and south Delta moving westward. But a large portion of that inflow is diverted south into the Head of Old River toward the pumping plants (Figure 6).

Figure 1. Approximate flood tide flow in cubic feet per second in mid to late January 2016. Blue arrows represent high Sacramento River, San Joaquin River and Mokelumne River flows (during flood tides). Red arrows depict negative flows of incoming tides. Note the south Delta incoming tide of -20,000 cfs would be less if not for the 14,000 cfs export rate at the south Delta pumping plants.

Figure 1. Approximate flood tide flow in cubic feet per second in mid to late January 2017. Blue arrows represent high Sacramento River, San Joaquin River and Mokelumne River flows (during flood tides). Red arrows depict negative flows of incoming tides. Note the south Delta incoming tide of -20,000 cfs would be less if not for the 14,000 cfs export rate at the south Delta pumping plants.

Figure 2. San Joaquin River flow at Mossdale at the head of the Delta upstream of Stockton and the Head of Old River. Note that on Jan 6 when flow reached about 6,000 cfs, the tidal signal dissipated when flow overcame the tidal forces.

Figure 2. San Joaquin River flow at Mossdale at the head of the Delta upstream of Stockton and the Head of Old River. Note that on Jan 6 when flow reached about 6,000 cfs, the tidal signal dissipated when flow overcame the tidal forces.

Figure 3: Flow from the Calaveras River, upstream of the Delta. The Calaveras enters the Delta at Stockton.

Figure 3: Flow from the Calaveras River, upstream of the Delta. The Calaveras enters the Delta at Stockton.

Figure 4. Release from Camanche Dam to the Mokelumne River. CDEC does not show flow values for the Mokelumne at gages further downstream. The Mokelumne enters the Delta near Jersey Point.

Figure 4. Release from Camanche Dam to the Mokelumne River. CDEC does not show flow values for the Mokelumne at gages further downstream. The Mokelumne enters the Delta near Jersey Point.

Figure 5. Cosumnes River flow well upstream of the Delta. Much of the high flow peaks enters the river’s connected floodplain, roughly between Lodi and Elk Grove, and does not flow immediately to the Delta. Flows in the Cosumnes enter the Mokelumne before passing into the Delta

Figure 5. Cosumnes River flow well upstream of the Delta. Much of the high flow peaks enters the river’s connected floodplain, roughly between Lodi and Elk Grove, and does not flow immediately to the Delta. Flows in the Cosumnes enter the Mokelumne before passing into the Delta

Figure 6. Flow entering the entrance to Old River from the San Joaquin River near Stockton.


Figure 6. Flow entering the entrance to Old River from the San Joaquin River near Stockton.

  1. https://www.usbr.gov/mp/cvo/vungvari/dsmeltsplitdly.pdf Note: website has changed to this new site. ↩

More on Delta Science

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More Delta ScienceI have written often on Delta science and what has been or could be learned from science to support water management.  Yet another biennial Delta science conference, the 9th, was held this past November.  This year’s conference theme was: “Science for Solutions:  Linking Data and Decisions.”  Another year has passed, and more has been studied and learned.  More dots have joined the dozens of previous dots in data charts from annual surveys of Delta organisms and habitat conditions.  More dots lament the loss of water and habitat.  The huge Delta Science Program has progressed yet another year.

Opening Talk

In Phil Isenberg’s opening talk, “A Guide for the Perplexed”, the former legislator and former chair of the Delta Stewardship Council suggested that scientists learn to smile more.  He asked: “Why should science be involved in policy anyway?”  He talked about how policy makers view science.  (Obviously, many are perplexed.)  He forgot that the universe and Mother Nature are vastly mysterious things, which are often more complicated than human understanding, but sensitive to human actions at the same time.  Yes, science is perplexing.

Mr. Isenberg talked about “independent science” and “combat science,” as though they were two different things.  To borrow a legal term, science is not self-executing.  Then he asked: “How do we know when we are using the best-available science”?  His answer: “When it is good enough to avoid doing something stupid.”  Clearly, we have yet to reach that point.  The problem has been in choosing to do the best thing, not that good choices or unknown or not “available.”  He then quoted Churchill:  “America will always do the right thing after trying everything else first”.  At least we have gotten past the point where we thought the world is flat.  It is all very perplexing.

Mr. Isenberg concluded by suggesting: “It’s the notion that scientists live looking farther out than the rest of us do with the gift of foresight that if properly utilized, can inform, educate, and ultimately motivate policy makers.”   He forgets that ultimately policy makers must trust scientists to get the job done.  Example: the Trinity Project and the atomic bomb in the 1940’s.  As long as water managers and policy makers lead the science, the Delta’s problems will not be solved.

The Delta Science Program

Clifford Dahm, former lead scientist for the Delta Stewardship Council, spoke on his Delta Science Program, which was forced upon us in the 2009 Delta Reform Act to ensure water and environmental policy are guided by the “highest caliber” science.  He spoke on the program’s Independent Science Board, outsiders who meet once a year to review “our science”.  He spoke on their Adaptive Management Program, which ensures that we evaluate everything and learn nothing.  He spoke on the program’s efforts to coordinate science and inform decision makers, and to develop and implement the Delta Science Plan and promote the Science Action Agenda.  He talked about their modeling efforts: “There’s just a lot of ways that modeling could be moved forward, and I hope that in the next two years, we can actually come back to you and say that some of our modeling efforts have shown greater fruition as time goes on.  We were talking about the idea of potentially a modeling center or a co-laboratory to get modelers together.”  Those would be the two years after which we will have new water quality standards, new biological opinions, and new tunnel-boring machines in the Delta, as well as several newly extinct native fish species.  They would also be the two years after 20 years of effort starting with the CalFed Bay-Delta Program.

A Great Question

U.C. Davis fisheries biologist Peter Moyle then addressed the question:  “How has your research program and the data it has produced over the last 35 years been used to develop solutions for conserving aquatic resources in Delta?”  He quoted the 1998 Strategic Plan:

This strategic plan, if followed, should lead to an orderly and successful program of adaptive ecosystem restoration….  The Strategic Plan Core Team has high expectations for the Ecosystem Restoration Program.  There is no turning back and the team anticipates that in 20-30 years many habitats will be restored, endangered species will become abundant enough to be delisted, and conflicts will be lessened , even in the face of population growth and increasing demands on resources.

In addressing the posed question, he then remarked:

In retrospect, now that almost 20 years has past since that was written, the statement almost seems tongue in cheek because clearly that has not happened.  I continue to help write reports that recommend how to improve the Delta ecosystem and frankly I don’t see much progress being made, as the delta smelt trends so eloquently attests…  the reality is that the Delta has continued to deteriorate as a habitat for native fishes, despite my research and despite many proposals for solutions.

His experience, like that of so many other long-time Delta scientists, is that few if any of the specific recommendations in the Strategic Plan have been implemented or completed.  Science has done its job, and scientists have long awaited action.  Policy makers and managers have failed us, not the science.

The use of science in complex public policy decision making

Chair of the State Water Board Felicia Marcus spoke on the use of science in decision making.  She suggested to scientists:  “Dare to recommend, but don’t decree …  Retain your scientific integrity but dare to make recommendations.  At the same time, own your power and be responsible with it and have empathy for the decision makers who have to balance, even as you would have them respect you.”  This is a very tough sell for scientists who have not been listened to for decades.  What will she and her Board do with two more rounds of recommendations on the Delta tunnels and the Bay-Delta Plan?  Will her Board be as transparent and methodical in their balancing as the scientists are in making their recommendations?

Chair Marcus further stated:

We’re entering the era of adaptive management that requires all of the above as well as integrating social sciences into our work … To make adaptive management work, we all have to learn how to be better ‘egosystem’ managers in order to be better ecosystem managers in the real world over time, versus lurching from sound bite to sound bite or wringing our hands that other players just don’t get it.

Sorry, but that’s not the problem.  It gives the policy makers and the managers too much credit and scientists too little.  Very few scientists think that managerial ignorance or lack of cognition is the biggest problem.  Rather, it’s that scientists have endured decades of adaptive management in which their lessons and caveats have on the whole been subsumed to the social sciences of politics and economics.  There are plenty of scientists throughout the resource agencies and non-profit groups who are extremely articulate and who have great senses of humor and social skills.   That hasn’t changed the outcomes: fish and other parts of the Bay-Delta aquatic ecosystem are in crisis, and the agricultural economy and other values against which the ecosystem is “balanced” are thriving..  And that balance sheet is really nothing to smile about.

Delta Smelt at Risk – 1/5/17

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The conflict continues between the Smelt Working Group (SWG) and the designated protector of the Delta smelt, the US Fish and Wildlife Service (FWS), over the amount of Delta exports allowed under existing Delta conditions.  The SWG recommends exports of no more than 2000 cfs, while the FWS continues to allow exports of 5000-6000 cfs (about half capacity), contrary to  the rules for Delta exports in its own smelt biological opinion.  The SWG notes that adult smelt continue to be captured in trawls in the central Delta (in surprising numbers), where smelt are at high risk of being drawn to the south Delta pumping plants or of eventually spawning in the central Delta where their offspring will be vulnerable to the export pumps.  The FWS is committed to allowing moderate exports as long as no adults are captured at the pumping plants’ fish salvage facilities (which would indicate it is too late to do anything other than to shut down the pumps). The National Marine Fisheries Service limits exports to the present 5000-6000 cfs level as of January 1, consistent with rules in its own biological opinion to protect juvenile salmon migrating down the Sacramento River.

Despite high Sacramento River inflows into the Delta of 30,000 to 50,000 cfs in the past two weeks, the smelt move from the Bay into the Delta by surfing the tides – that is, by moving upstream on incoming tides.  Flood tide velocities shown in Figure 1 indicate the adult smelt can readily “surf” into the Delta until they come up against the strong flows of the Sacramento River and its inflow channels that overwhelm the tidal flows.  In the south Delta, where limited flow has been coming down the San Joaquin River, export pumping plants accentuate the negative flood tide velocities and reduce ebb tide velocities.  This further increases the risk that adult smelt will be drawn to the south Delta.  Only time will tell if this risky FWS strategy protects the endangered Delta smelt during this potential comeback year.

Figure 1. Flood tide channel current velocities in feet/second in early January 2017. Arrows depict current direction on flood tides. Sacramento River net downstream flow was 30,000-50,000 cfs, which overwhelmed the flood tide. Light blue dots are flow gaging stations. Basemap source with gaging stations is DWR/CDEC.

Figure 1. Flood tide channel current velocities in feet/second in early January 2017. Arrows depict current direction on flood tides. Sacramento River net downstream flow was 30,000-50,000 cfs, which overwhelmed the flood tide. Light blue dots are flow gaging stations. Basemap source with gaging stations is DWR/CDEC.

Delta Smelt Status – End of 2016

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The Delta smelt population in the Bay-Delta reached record or near-record low indices in 2016 (Figures 1-3), but ended the year with some promise of recovery (Figure 3). The December 2016 Kodiak Trawl Survey collected 214 Delta smelt in one of its nine trawls, and at least one Delta smelt was captured in each of the other eight trawls. Fall 2016 has been wet following a below normal water year 2016 (October 2015 – September 2016), which followed the 2012-2015 drought.

Some early insight into this apparent resurgence in the 2017 index can be gained by reviewing the relationship between the Fall Midwater Fall Index and the subsequent Winter Kodiak Trawl Index (Figure 4). There is a strong positive stock (previous fall index) to recruitment (winter index) relationship with three apparent outliers (2009, 2016, 2017). The poor fall 2015 and 2016 indices resulted in strongly contrasting winter recruitment (winter 2016 and 2017 indices). This likely reflects the benefits of a wet fall of 2016 to the 2017 index (Dec. 2016 survey), as compared to the dry fall of 2015 and subsequent poor 2016 index.

Water year 2015 was a critically dry year with extremely low flows. In contrast to 2015, critically dry year 2008 with its low fall index produced a strong winter 2009 index. The strong showing in the winter of 2009 may have been due to the extremely low December (2008) and January (2009) exports, combined with relatively high Delta outflow pulses, a pattern that rarely occurs after a critically dry year. We will be keeping a close look at how the apparent resurgence plays out in 2017, especially with new less stringent export restrictions mandated in recent legislation for the implementation of the two federal biological opinions that apply to Delta water project operations.

Figure 1. Summer Townet Index for Delta smelt 1969-2016.

Figure 1. Summer Townet Index for Delta smelt 1969-2016.

Figure 2. Fall Midwater Trawl Index for Delta smelt 1967-2016.

Figure 2. Fall Midwater Trawl Index for Delta smelt 1967-2016.

Figure 3. Winter Kodiak Trawl Index of Delta smelt 2002-2016, including December 2016 (Water Year 2017). December surveys were not conducted from 2002 to 2014.

Figure 3. Winter Kodiak Trawl Index of Delta smelt 2002-2016, including December 2016 (Water Year 2017). December surveys were not conducted from 2002 to 2014.

Figure 4. Winter Kodiak Trawl Index versus previous fall Midwater Trawl Index of Delta smelt (log scales) 2002-2016. The 2017 winter index is from Dec 2016 survey only and does not include Jan-Mar 2017 survey results as yet, thus it will likely be even higher than shown.

Figure 4. Winter Kodiak Trawl Index versus previous fall Midwater Trawl Index of Delta smelt (log scales) 2002-2016. The 2017 winter index is from Dec 2016 survey only and does not include Jan-Mar 2017 survey results as yet, thus it will likely be even higher than shown.

“Robust” San Joaquin Salmon Runs

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The San Joaquin River appears to be seeing a boon in salmon runs this year despite the recent drought. Editor Dennis Wyatt of the Manteca Bulletin suggested on December 14 that “robust” salmon runs on the San Joaquin River in recent years “discredit” state claims that more of unimpaired flow of the Stanislaus, Tuolumne, and Merced rivers should be passed to the Bay-Delta:

Spawning adult numbers after being in the 1,000 to 2,000 range from 2006 through 2011 now consistently surpass 5,000 despite the drought. The scientific research conducted by FISHBIO over the past decade and underwritten by the South San Joaquin Irrigation District and Oakdale Irrigation District is being used by the two water agencies to discredit state claims that the only way to increase salmon on the Stanislaus River — and the neighboring Tuolumne and Merced rivers — is by ratcheting up unimpaired flows to 40 percent between February and June. 1

This theory is circulating among supporters of water purveyors who draw water from the Stanislaus. For example, Mr. Wyatt’s editorial was reproduced verbatim on Congressman Jeff Denham’s website.2

One of the main reasons for the recent decade of run increases is most likely increases in flow requirements in the spring and fall as mandated in the National Marine Fisheries Service’s 2009/2011 biological opinion for the Central Valley Project. It is more logical that further flow improvements would lead to further salmon enhancements, perhaps even approaching target levels specified in the Central Valley Project Improvement Act of 1992 (CVPIA).

There is a long way to go. The so-called robust runs are far below the CVPIA target of 78,000 salmon for the San Joaquin, numbers that were most recently achieved in Water Year 2000 (Figure 1). While there have been improvements during the last ten years, eight of which were drought years (Figure 2), runs are still about 70,000 fish short of the doubling goal.

In addition, much of the recent improvement is related to increased hatchery production from the state hatcheries on the Mokelumne and Merced rivers (Figure 3). Hatchery production also benefits from trucking hatchery smolts to the Bay. Runs in the Stanislaus and Tuolumne also benefit from strays from the two hatcheries. The CVPIA doubling goal is for natural production.

Finally, there needs to be defined fall flow pulses in addition to higher spring flows. Fall pulse flows reduce water temperature in the three tributaries and mainstem during the fall migration period. In the past, drought year fall flows were depressed (Figure 4). This made it harder for fish to find the San Joaquin tributaries and led to high fall water temperatures (Figure 5). High temperatures can block or hinder adult salmon migration, reduce adult pre-spawn survival, and lower egg viability. Lack of fall flow pulses in 2014 and 2015 led to poor salmon escapement, especially in the Tuolumne and Merced Rivers. Higher flows and lower water temperatures in the Stanislaus in 2015 likely led to a greater proportion of the overall San Joaquin run choosing the Stanislaus River (Figure 2). Fall flows from tributary reservoirs should be sufficient to maintain tributary water temperature below 60°F and San Joaquin River temperatures below 65°F. These goals are achievable in most water years, and were for the most part achieved in the San Joaquin River in October, 2016 (Figure 5).

Sorry, folks. Flow matters.

Figure 1. San Joaquin salmon production 1957-2010 as related to flow two years earlier. Source: Appendix C, SWRCB 2012.

Figure 1. San Joaquin salmon production 1957-2010 as related to flow two years earlier. Source: Appendix C, SWRCB 2012.

Figure 2. Salmon run totals (escapement) from the Stanislaus, Tuolumne, and Merced rivers 2005-2015. Data source: CDFW.

Figure 2. Salmon run totals (escapement) from the Stanislaus, Tuolumne, and Merced rivers 2005-2015. Data source: CDFW.

Figure 3. San Joaquin salmon escapement from 2008 to 2015. Source: CDFW.

Figure 3. San Joaquin salmon escapement from 2008 to 2015. Source: CDFW.

Figure 4. San Joaquin River flow 2003-2016 at Vernalis (downstream of confluence with Stanislaus, Tuolumne, and Merced rivers). Red circles denote drought years lacking adequate fall flow prescriptions.

Figure 4. San Joaquin River flow 2003-2016 at Vernalis (downstream of confluence with Stanislaus, Tuolumne, and Merced rivers). Red circles denote drought years lacking adequate fall flow prescriptions.

Figure 5. Fall water temperature of San Joaquin River at Vernalis in 2015 (top) and 2016 (bottom). Red circles denotes key salmon migration period when fall flow prescriptions occur. Note higher water temperature in 2015 compared to 2016, which had higher fall flows. Source: CDEC.

Figure 5. Fall water temperature of San Joaquin River at Vernalis in 2015 (top) and 2016 (bottom). Red circles denotes key salmon migration period when fall flow prescriptions occur. Note higher water temperature in 2015 compared to 2016, which had higher fall flows. Source: CDEC.