Welcome to the California Fisheries Blog

The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.

An Unprecedented Experiment – July 2016

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“State’s Delta smelt plan calls for more water flowing to sea” – This headline to a recent Sacramento Bee article speaks of the state and federal governments’ hope to get more water for Delta outflow to the Bay this summer to help Delta smelt after four devastating drought years.  Smelt are at record lows, and their endangered status under the state and federal endangered species acts requires an effort to help recover them.  When the Delta smelt plan was announced, this year’s Summer Delta Smelt Index had just come in at 0.0, the same as it was last summer.

A grand experiment began on July 15.  With Shasta Reservoir releases held low to save cold water for salmon, more Delta outflow for the experiment was provided by reducing exports from 9000 cfs to 2000 cfs.  Deliveries to South-of-Delta CVP and SWP contractors were cut to a minimum, even though the plan had promised: “[no] cuts to water supply planned.”

Conditions on July 12 can be seen in Figure 1.  Reservoir releases and some natural river flow totaled approximately 30,000 cfs.  Most (80%) of the 20,000 cfs of Delta inflow was coming from Oroville and Folsom reservoirs.  Of that amount, only 7000 cfs was leaving the Delta for the Bay (the required minimum outflow in July of a Below Normal year under state standards is 6500 cfs).  Approximately 6,000 cfs was being diverted from the upper Sacramento River below Redding.  Another 3,000 cfs was being diverted from the lower river and its tribs.  Another 4,000 cfs was diverted in the Delta.  Finally, the state SWP was pumping 7000 cfs and federal CVP was pumping 1000 cfs from the south Delta.

By July 15, conditions in the Delta changed.  Delta outflow doubled, while exports were reduced by 80% (Figure 2).

We often hear about “adaptive management” to test things to see if they help or not.   This is a big, very unprecedented adaptive management experiment.  The purpose is to help Delta smelt recover from a dramatic decline over the past two decades.  However, it will be difficult to help what is not there. There were few smelt out there a month ago; hopefully, there are still enough that the experiment will make a difference.

The important thing now with such an experiment is to make sure we learn everything we can from it.  The following are some questions that should be addressed.

  1. What changes occur in flow, nutrients, salinity and water temperature in the Delta and Bay?
  2. If there are no Delta smelt, what changes occur to the other pelagic organisms such as phytoplankton, zooplankton, shrimp, longfin smelt, striped bass, herring, anchovy, and threadfin shad?
  3. Will the change stimulate a plankton bloom that benefits the Bay-Delta estuary?

From the point of view of managing the experiment, it is good that other important factors such as Delta inflow remain unchanged, so that there are not too many variables to filter out as determinative in any response.  It will be difficult enough to determine the relative importance of higher outflow versus lower export.

Hydrology

Preliminary results indicate that the experiment (as expected) had a noticeable effect on Delta hydrology.  By July 24, outflow had dropped back from its peak during the experiment of 14,000 cfs to 9000 cfs (Figure 3), as exports were again increased to about 7000 cfs, as shown in Old and Middle River tidally averaged flow (Figure 4).  Net lower San Joaquin River flow at Jersey Point initially increased sharply in response to the reduced exports (Figure 5).  The net flows diverted from the lower Sacramento to the lower San Joaquin via Threemile Slough were also reduced (Figure 6).

Salinity

Salinity (EC) eventually responded to the higher outflows as the pulse of freshwater pushed westward.  Salinity on the lower Sacramento at Emmaton (Figure 7) and Jersey Point on the lower San Joaquin (Figure 8) declined measurably.  Salinity also declined downstream at the confluence of the two rivers near Collinsville in eastern Suisun Bay (Figure 9).

Water Temperature

There has been slightly lower water temperature in the western Delta.  This is at least partially explained by cooler air temperatures during the experiment.  The water temperature at X2 (location of 2 ppt salinity or 2700 EC declined as X2 was located on-average further west during the experiment  (Figure 10).  However, that too could be explained by lower air temperatures.

Plankton Blooms

So far there is no evidence of enhanced plankton production by the experiment.  There has been little change in chlorophyll measured at selected gaging stations in the central and west Delta.

Fish

While results of Delta-wide fish surveys will not be available for some time, results of export salvage of two pelagic Delta species, striped bass and threadfin shad, showed sharp reductions as expected (Figures 11 and 12).

Figure 1. Water conditions in mid July 2016 in the Sacramento Valley and Delta before the experiment. Red denotes major water releases in cfs from the Valley’s four largest reservoirs. Blue denotes three key river flow locations: lower Sacramento River upstream of the Feather River, Freeport coming into the Delta, and Delta outflow. Green denotes south Delta exports.

Figure 1. Water conditions in mid July 2016 in the Sacramento Valley and Delta before the experiment. Red denotes major water releases in cfs from the Valley’s four largest reservoirs. Blue denotes three key river flow locations: lower Sacramento River upstream of the Feather River, Freeport coming into the Delta, and Delta outflow. Green denotes south Delta exports.

Figure 2. Flow conditions in the Sacramento Valley and Delta on 20 July 2016. Delta outflow is 14,000 cfs. Sacramento River flow above the mouth of the Feather River was 4,000 cfs. Sacramento River inflow to the Delta at Freeport is 19,000 cfs. (Note total Delta inflow was about 20,000 cfs. Total Central Valley reservoir releases and uncontrolled river inflows was over 30,000 cfs.). About two-thirds of the Delta inflow came from Feather Riverand American River reservoirs. Though only 2000 cfs was being exported from the south Delta projects, approximately 14,000 cfs of Sacramento Valley reservoir releases were being diverted for water supply from Sacramento Valley rivers and the interior Delta. Nearly all San Joaquin Valley reservoir releases were being diverted.

Figure 2. Flow conditions in the Sacramento Valley and Delta on 20 July 2016. Delta outflow is 14,000 cfs. Sacramento River flow above the mouth of the Feather River was 4,000 cfs. Sacramento River inflow to the Delta at Freeport is 19,000 cfs. (Note total Delta inflow was about 20,000 cfs. Total Central Valley reservoir releases and uncontrolled river inflows was over 30,000 cfs.). About two-thirds of the Delta inflow came from Feather Riverand American River reservoirs. Though only 2000 cfs was being exported from the south Delta projects, approximately 14,000 cfs of Sacramento Valley reservoir releases were being diverted for water supply from Sacramento Valley rivers and the interior Delta. Nearly all San Joaquin Valley reservoir releases were being diverted.

Figure 3. Delta outflow increased to 14,000 cfs during the July 15-23 experiment.

Figure 3. Delta outflow increased to 14,000 cfs during the July 15-23 experiment.

Figure 4. The tidally filter flow in the central Delta showed about a 6500 cfs reduction in the flow in Old and Middle River toward the south Delta export pumps.

Figure 4. The tidally filter flow in the central Delta showed about a 6500 cfs reduction in the flow in Old and Middle River toward the south Delta export pumps.

Figure 5. The experiment brought a sharp response in the tidally filtered flow at Jersey Point in the lower San Joaquin River in the western Delta.

Figure 5. The experiment brought a sharp response in the tidally filtered flow at Jersey Point in the lower San Joaquin River in the western Delta.

Figure 6. The experiment brought a reduction in net flows pulled from the lower Sacramento River to the lower San Joaquin via Threemile Slough.

Figure 6. The experiment brought a reduction in net flows pulled from the lower Sacramento River to the lower San Joaquin via Threemile Slough.

Figure 7. Salinity (EC) at Emmaton on the lower Sacramento River just north of Antioch 14-24 July, 2016.

Figure 7. Salinity (EC) at Emmaton on the lower Sacramento River just north of Antioch 14-24 July, 2016.

Figure 8. Salinity (EC) at Jersey Point on the lower San Joaquin River near Antioch 14-24 July, 2016.

Figure 8. Salinity (EC) at Jersey Point on the lower San Joaquin River near Antioch 14-24 July, 2016.

Figure 9. Salinity (EC) at Collinsville near the confluence of the lower Sacramento and San Joaquin channels in eastern Suisun Bay 14-24 July, 2016.

Figure 9. Salinity (EC) at Collinsville near the confluence of the lower Sacramento and San Joaquin channels in eastern Suisun Bay 14-24 July, 2016.

Figure 10. Water temperature (F) at Collinsville in eastern Suisun Bay 14-24 July, 2016. Red dots indicate water temperature when X2 was located at Collinsville

Figure 10. Water temperature (F) at Collinsville in eastern Suisun Bay 14-24 July, 2016. Red dots indicate water temperature when X2 was located at Collinsville

Figure 11. Salvage of striped bass at south Delta export facilities July 1-20, 2016.

Figure 11. Salvage of striped bass at south Delta export facilities July 1-20, 2016.

Figure 12. Salvage of threadfin shad at south Delta export facilities July 1-20, 2016.

Figure 12. Salvage of threadfin shad at south Delta export facilities July 1-20, 2016.

State Comes Through With Lower Exports

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On July 12, the State came out with its plan to save smelt by reducing Delta exports and increasing Delta freshwater outflow. The next day, exports were increased 1000 cfs (from 8000 to 9000 cfs) and outflow was reduced 1000 cfs to 3000 cfs as measured by USGS. But on July 17, the State finally came through. The State dropped State Water Project (SWP) exports from 7000 to 4000, and the feds dropped Central Valley Project (CVP) exports from 1,600 to 800. Then on July 19, combined exports dropped another 3000 cfs, to less than 2000 cfs. Delta outflow is now nearly 14,000 cfs, the level it was in late July 2011, the last wet year. Though the change may have come too late, we will see come fall any response in the indices for longfin smelt and Delta smelt.

The flow response showed up immediately in flow gages in Old and Middle Rivers, where flows of minus 11,000 dropped to minus 5,000 cfs (Figure 1). The response in salinity levels will take a few days, but it’s already showing up in the western Delta at False River (Figure 2) and Jersey Point (Figure 3). Even in the smaller confines in False River, the effect of the change is hard to perceive over the effect of tides (Figure 4), but it is there. Eventually, the higher freshwater outflow will push the salt westward.

The first measure of progress should appear in surveys 5 and 6 of the Summer Townet Survey. Because there are few smelt left from which to observe a response, a response will be most noticeable in striped bass. We should be able to see a change to a more westward distribution of the Low Salinity Zone and striped bass juveniles (Figure 5).

Flow Graph

Figure 1. Hourly flow in Old and Middle Rivers combined in the central Delta from July 8 to July 18, 2016.

Salinity graph

Figure 2. Salinity (EC) in False River in western Delta from July 8 to July 18, 2016.

Electrical conductivity graph

Figure 3. Salinity (EC) in lower San Joaquin River at Jersey Point in western Delta from July 8 to July 18, 2016.

Flow Graph

Figure 4. Hourly flow in False River in western Delta from July 8 to July 18, 2016.

Map of striped bass choice

Figure 5. Townet survey 1 catch of striped bass June 2016.

Increasing Salmon Rearing Habitats in the Upper Sacramento River – A Long-Overdue Management Action

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Large amounts of rearing habitats for young salmon were lost in the upper Sacramento Valley Basin when Shasta and Keswick Dams were built. Loss of this rearing habitat (located in smaller, shallower river channels upstream of the dams – like the McCloud River) was considered one of the numerous reasons for the listing of the winter-run Chinook as endangered. Since dam construction, young salmon emerging from main-stem spawning areas downstream of the dams must now contend with the severe rigors of a large, deep river channel. It is generally acknowledged that the quality of rearing habitats in those upstream areas was superior to habitats below the dams (Vogel 2011).

Although significant efforts have been made to increase the quantity and quality of spawning habitats below the dams, minimal progress has occurred on rearing habitats. Massive amounts of spawning gravels have been added to the upper Sacramento River downstream of Keswick Dam, but there are indications that rearing habitats may be an equally important, if not more-important, factor limiting the fish populations. As pointed out by the U.S. Fish and Wildlife Service (USFWS),“ … there would be little value in increasing the quantity of available spawning gravel if the problem that actually limits juvenile production is lack of adequate rearing habitat” (USFWS 1995). Astonishingly, more than two decades later and despite over 1 billion dollars spent on salmon restoration, that potential dilemma remains unresolved.

Present-day rearing habitats are considered very limited and predation during juvenile rearing is believed to be a stressor of very high importance (NMFS 2014). The best habitats, in conventional theory, would be on the channel fringes. Indeed, some such areas with desirable attributes do exist, but are sparse. However, due to the nature of the river reach where most winter-run salmon spawn in deep water, many of the ideal habitat characteristics for rearing are lacking (e.g., appropriate velocities and cover). Subsurface structures like woody debris are severely deficient and would be challenging to restore due to lack of significant recruitment and periodic extremely high-flow events (Shasta Reservoir flood-control releases) that would dislodge this essential feature. In many areas where salmon spawn, the river is wide (e.g., 500 feet) and channel edges are deep (Figure 1). Fry emerging from redds in the main-stem riverbed encounter a paucity of velocity and predator refugia. Underwater observations and sonar camera footage near artificial structures in deep water (e.g., bridge piers) have frequently shown extensive salmon rearing activity, but may suggest the fish are utilizing those areas because insufficient other natural structures on the riverbed are limited or absent (Vogel 2011).

Figure 1. Cross-sectional profile of the upper Sacramento River in an area 500 feet wide and 10 feet deep (scale is approximate).

Figure 1. Cross-sectional profile of the upper Sacramento River in an area 500 feet wide and 10 feet deep (scale is approximate).

Based on many years of observations in the main-stem Sacramento River, large schools of young salmon exhibit a very strong affinity for specific habitats unique in a large, deep river channel. This circumstance is a quandary for salmon fry upon emergence from redds positioned in deep water and long distances from channel edges. The weak-swimming fry are immediately exposed to high near-bed water velocities and minimal refugia to escape from predatory fish such as rainbow trout that are very abundant in areas where winter-run Chinook spawn. The region where young salmon have been observed in deep channel areas include behind tail spills of redds and bridge piers, and in eddies adjacent to vertical bedrock walls. It is particularly evident that large schools of salmon choose areas where eddies exist adjacent to high water velocity shear zones. This provides the fish necessary velocity refugia while simultaneously gaining ready access to drift food organisms, thereby minimizing energy expenditure. Unfortunately, those same areas do not provide refuge from predatory fish.

The following are examples of salmon rearing in the deeper waters of the upper Sacramento River. [It must be noted that an enormous amount of sonar camera footage (not shown here) has been taken along near-shore shallow areas that did not show significant rearing utilization.] After viewing each video, stop or click “cancel” on the YouTube player to allow viewing of subsequent videos in this blog entry. For the sonar camera footage, juvenile Chinook can be discerned by largely maintaining their positions in the current, exhibiting visible swimming movements. Ensonified objects moving with the current are debris drifting downstream (e.g., algae and weed fragments).

  • A school of winter-run Chinook fry rearing on the riverbed adjacent to an Interstate-5 bridge pier and woody debris in the Sacramento River at water depths of 10 feet: http://www.youtube.com/watch?v=BP_szST5REo&NR=1
  • School of juvenile Chinook salmon rearing behind a Lake Redding bridge pier in the Sacramento River at water depths approximately 10 feet deep: https://youtu.be/g0dFA8V4-sc
  • School of juvenile Chinook salmon rearing in the Sacramento River in very deep water alongside a vertical bedrock wall and behind woody debris and filamentous algae or weeds: https://youtu.be/Tv0TtOCdzNY
  • School of juvenile Chinook salmon rearing in the Sacramento River behind the remnants of a concrete bridge pier on the riverbed in water depths approximately 12 feet deep with a large fish swimming through the school: https://youtu.be/uAT9Wkx-nSY

An action identified in the 2014 National Marine Fisheries Service (NMFS) Salmon Recovery Plan is: “Using an adaptive management approach and pilot studies, determine if instream habitat for juvenile salmon is limiting salmonid populations, by placing juvenile rearing-enhancement structures in the Sacramento River.” Evaluation of such measures is also a priority in the USFWS Anadromous Fish Restoration Program (USFWS 2001). Most recently, NMFS (2016) identified “a lack of suitable rearing habitat in the Sacramento River” as an “important threat” to winter-run Chinook. Therefore, a proposal to place rearing habitat structures in some deeper-water areas (approximately > 8 feet) of the main-stem upper Sacramento River was recently developed. Using guidance from the California Department of Fish and Wildlife’s (CDFW) Stream Habitat Restoration Manual (CDFW 2010), woody debris heavily anchored to the riverbed using large, angular boulders has been recommended for this initial step and has received favorable response from the fishery resource agencies. Angular boulders would provide the dual benefits of firmly securing woody debris and providing velocity refugia for young salmon; woody debris would provide predator refugia.

It is important to emphasize that this proposal is a pilot project and not intended to create nearshore, shallow-water habitat attributes similar to those that existed in upstream areas prior to dam construction or were lost in downstream riparian areas afterwards. There are already separate plans to construct small, shallow-water side channels in the main-stem river to address that issue. In contrast, this project is intended to place structures in completely different rearing habitat zones in deeper water where large numbers of young salmon have been observed. Given the ecological realities of the specific and unique environmental conditions in the upper Sacramento River, deep-water rearing habitats could very well be one of the most important environmental variables affecting the survival of main-stem spawning salmon progeny. If the pilot project determines high rearing utilization, the project could easily be expanded.

Sites chosen for rearing habitat placement should be in the vicinity and downstream of known spawning sites that are currently lack good rearing habitats. To provide the most benefit to young salmon, placement of rearing structures is focused on the approximate 12-mile reach of the upper Sacramento River below Keswick Dam. This area is where nearly all the endangered winter-run Chinook have been spawning in recent years and also supports the other three Chinook runs as well as the threatened steelhead.

Hopefully, a pilot project will be implemented in early 2017 … stay tuned.

Literature Cited

California Department of Fish and Wildlife. 2010. California Salmonid Stream Habitat Restoration Manual. July 2010. http://www.dfg.ca.gov/fish/Resources/HabitatManual.asp

National Marine Fisheries Service. 2014. Recovery plan for the Evolutionarily Significant Units of Sacramento River winter-run Chinook salmon and Central Valley spring-run Chinook salmon and the Distinct Population Segment of California Central Valley steelhead. California Central Valley Area Office. July 2014. 406 p. http://www.westcoast.fisheries.noaa.gov/publications/recovery_planning/salmon_steelhead /domains/california_central_valley/final_recovery_plan_07-11-2014.pdf

NMFS. 2016. Species in the Spotlight. Priority Actions: 2016 – 2020. Sacramento River Winter-Run Chinook Salmon, Oncorhynchus tshawytscha. 16 p.
http://www.nmfs.noaa.gov/stories/2016/02/docs/sacramento_winter_run_chinook _salmon_spotlight_species_5_year_action_plan_final_web.pdf

U.S. Fish and Wildlife Service. 1995. Working paper: habitat restoration actions to double natural production of anadromous fish in the Central Valley of California. Volume 1. May 9, 1995. Prepared for the U.S. Fish and Wildlife Service under the direction of the Anadromous Fish Restoration Program Core Group. Stockton, CA. https://www.fws.gov/lodi/anadromous_fish_restoration/documents/WorkingPaper_v1.pdf

U.S. Fish and Wildlife Service. 2001. Final Restoration Plan for the Anadromous Fish Restoration Program. A plan to increase natural production of anadromous fish in the Central Valley of California. Released as a revised draft on May 30, 1997 and adopted as final on January 9, 2001. 106 p. plus appendices. https://www.fws.gov/cno/fisheries/CAMP/Documents/Final_Restoration_Plan_for_the_AFRP.pdf

Vogel, D.A. 2011. Insights into the problems, progress, and potential solutions for Sacramento River basin native anadromous fish restoration. Report prepared for the Northern California Water Association and Sacramento Valley Water Users. Natural Resource Scientists, Inc. April 2011. 154 p. http://www.norcalwater.org/wp-content/uploads/2011/07/vogel-final-report-apr2011.pdf

Barging Hatchery Smolts to the Bay

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In this blog I often recommend barging hatchery and even wild salmon from spawning rivers to the Bay up to 200 miles or more over conventional trucking or direct releases from hatcheries. The theory is that continuous recirculation of water in the barge (or boat) holding tank helps the young salmon remember from where they came and imprint the route back to their home river or hatchery.  Trucking directly to the Bay is believed to cause straying to non-natal rivers, resulting unnatural mixing of stocks, hatchery fish straying into wild fish spawning rivers, and less salmon returning to their home hatcheries where their eggs may be needed to meet quotas.  It is well documented that trucking and pen acclimation significantly increases the contribution of hatchery smolts to the ocean fishery up to two or three fold or more.  Concern over straying has kept the practice to a minimum.

Well it turns out from studies conducted with tagged hatchery salmon beginning with releases in 2008 that trucking, at least of American and Feather hatchery smolts, does not lead to significant amounts of straying.  Also, barging does not significantly reduce the already low straying rate.  So trucking to Bay net pens for acclimation remains the chosen strategy for the two largest State hatcheries, and probably the other two on the Mokelumne and Merced rivers.

The jury is still out on the Coleman and Livingston Stone federal hatcheries near Redding.  Straying rates are higher and the benefits of trucking over 200 miles seem questionable.  One concern I have is the high straying rate encountered for Coleman (Battle Creek) fish includes fish that move past Battle Creek further up in the Sacramento River and its upper tributaries.  Most of the spawning fish in these areas come from Coleman and Livingston Stone national fish hatcheries.  Because Coleman was built to mitigate for the loss of fish to those areas, I question their inclusion in the straying estimates.  The USFWS, which manages the two hatcheries, continues to be reluctant to truck and barge fish.

Though barging may not be needed for the Feather and American River hatcheries, it still holds potential for improving survival and reducing straying overall.  So far, there is no evidence that barging improves survival over trucking to Bay net pens.  I reviewed subsequent tag returns for a barge release group in early May 2012 with returns from two net pen groups released at the same time in the Bay.  I found the subsequent return percentage of the barge group  to be in between the two trucked pen release groups.  In the notes of the barge release, high predation by birds was noted.  In the photo of a barge release below many birds can be seen.  I wonder if the barge release would also benefit from the same pen acclimation that is employed after trucking, which significantly improves trucked fish release survival and subsequent contribution to the fishery.  (Note: I have been present at numerous truck releases to the Bay and have observed obvious extreme predation on the disoriented and confused hatchery fish, often released into warmer, saltier water than was present at the hatchery by a horde of well-trained and waiting birds and predatory fish.  Release to net pens at variable locations for acclimation and tow to open waters for underwater release seemed to greatly reduce predation, which proved true in subsequent tag returns.)

A closer look at the tag-release-recovery data and further experimentation would better answer the questions, concerns, and hypotheses.  There were nine barged groups released into the Bay from 2012-2014.  With some tags still out or not processed (tags are in noses of adult fish returns 2-4 years after release), information continues to come in.  The nearly million or so coded-wire-tags released from the nine barge groups swam with approximately 30 million other tagged fish from the six Central Valley hatcheries.  Furthermore, records are meticulously kept with other tagged groups from Washington and Oregon, as well as from other California watersheds (e.g., Klamath), by the Pacific States Marine Fisheries Commission.  An example of the type of information available is shown in the map-chart below for just the one barge release group from 2012.  The California Department of Fish and Wildlife has its own team and program to keep track of California immense database on releases and recoveries.  The Department’s report from November 2015 provides an excellent review of the whole process and results to date.

Barge in SF Bay

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Managing the Delta in Summer to Protect Delta Smelt

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During June of this year, there was an effort on the part of the US Fish and Wildlife Service to procure water for summer Delta outflow for Delta smelt. Now the State has announced a similar plan. The summer standards for outflow in this Below Normal water year are a monthly average of 6500 cfs in July, 4000 cfs in August, and 3000 cfs in September. These outflows and the variability inherent in the monthly average standard are not protective of Delta smelt. In a June post, I recommended 9000, 5000, and 4000 cfs, respectively, to protect remaining smelt after four years of drought conditions. No water has been procured, and Delta outflow so far in July has averaged 7000 cfs.

The map below (Figure 1) shows the average location of X2, the location where salinity is approximately 2 parts per thousand (sea water is approximately 30 ppt) at various Delta outflows in cubic feet per second. X2 is the general location of the critical mixing zone of the estuary and the upper end of the Low Salinity Zone (1-6 ppt). The state Delta outflow standard for August is 4000 cfs, which should keep the daily average location of X2 west of Emmaton (EMM) and Jersey Pt (SJJ). This standard is required to protect Delta water quality, keep Delta smelt west of the influence of South Delta exports, and keep emigrating juvenile salmon moving west toward the Bay and Ocean. The standard applies in wetter year types including this year. In drier years, as in the past four years, the standard is 3000-3500 cfs.

The need for the higher July outflow protection stems from the fact that the smelt gradually move westward into more brackish water over the summer. In July they tend to be upstream of X2 in a planktonic stage and vulnerable to being drawn into the central Delta. They are often located at the upper end of the Low Salinity Zone (500-1500 EC) which in July, at 6500 cfs outflow, is vulnerable to exports (see location of Threemile Slough TSL, Jersey Pt SJJ, and False River FAL in Figure 1).

The issue of summer protections for smelt is critical to the future management prescriptions being developed in new water quality standards and smelt biological opinions. That makes it important to water contracting agencies like the Metropolitan Water District:

One of the key things the water contracting agencies are focusing on is the science behind the summer flow. “There’s been nothing that’s been articulated in writing in a comprehensive nature describing the science that leads to this proposal as to what kind of function is this summertime flow providing or what types of changes do they expect to occur for Delta smelt as a result of taking this kind of action,” he [Steve Arakawa, Bay Delta Initiatives Manager of Metropolitan Water District] said. “The water contracting agencies are following this very carefully because of the longer term implication of where such an action could show up in future regulations, whether it’s the biological opinions for the projects or whether it’s the State Water Resources Control Board setting standards and how Fish and Wildlife Service might be making proposals in future regulation proceedings.”… “There has been no clear indication of the science behind the flow proposal,” he said. “There have been discussions about turbidity, temperature, and salinity, but in many cases it’s mainly salinity that is affected by this flow. Whether turbidity or temperature can be affected by the flow is another question or maybe uncertain. Then it’s about with this additional flow, where do the fish go – do they stay in the Suisun Bay, do they go up into the channels into Suisun Marsh, farther up north? All of that is in question. The interest of the water contracting agencies is if this does proceed, is there a thought-out way of measuring the benefits of such proposed flows to monitor where do the fish go, what kind of results do we expect, and whether in fact those results did occur with such action.” 1

Figure 1. Location of X2 (2 parts per thousand salinity) in the Delta at various Delta outflows.

Figure 1. Location of X2 (2 parts per thousand salinity) in the Delta at various Delta outflows.

To protect Delta smelt in early summer (June and July), X2 and the Low Salinity Zone need to be located west of Emmaton and Jersey Point to ensure portions of the LSZ are not drawn into the central Delta from Jersey Point (via False River FAL) or Threemile Slough (TSL). In the following sections, graphs show clearly that such protections did not occur in drought years 2014 and 2015, and as yet not in 2016.

Keeping X2 below Jersey Point requires some daily, even hourly tuning of the Central Valley and Delta plumbing to compensate for tides. The next two charts (Figures 2 and 3) show that EC of 2000-4000 (X2 is about 2700 EC) reaches Jersey Point when tidally-filtered flow falls below zero during spring tides. The LSZ and X2 were at Jersey Point in early summer in both drought years.

Figure 2. Salinity (EC) in blue and tidally filtered flows in red at Jersey Point in early summer 2015. Delta outflows were 3000-4000 cfs in this critically dry year.

Figure 2. Salinity (EC) in blue and tidally filtered flows in red at Jersey Point in early summer 2015. Delta outflows were 3000-4000 cfs in this critically dry year.

Figure 3. Salinity (EC) in blue and tidally filtered flows in red at Jersey Point in early summer 2014. Delta outflows were 3000-5000 cfs in this critically dry year.

Figure 3. Salinity (EC) in blue and tidally filtered flows in red at Jersey Point in early summer 2014. Delta outflows were 3000-5000 cfs in this critically dry year.

In 2016 to date, by contrast, with outflow about 7000 cfs in early summer, salinity at Jersey Point is lower (Figure 4), but the upper LSZ remains at Jersey Point. Increasingly high salinity is indicative of rising south Delta exports through the period, beginning near 3000 cfs in early June and reaching 8000 cfs in early July. The tidally filtered flow at Jersey Point (Figure 5) gradually declined with increasing exports after mid-June.

In short, my recommendation for 9000 cfs outflow in July, and rationale for the quest for more water by the USFWS, are simply to bring salinity at Jersey Point back where it was in early June: below 500 EC. This would keep X2 and the LSZ with its remaining Delta smelt downstream of Jersey Point and away from the net negative flows toward the export pumps. Also, the further west X2 and the LSZ are located, the cooler they will be, which also benefits the smelt. If it were up to me, I would set a standard that EC should not exceed 500 at Jersey Point in early summer.

Figure 4. Salinity at Jersey Point in early summer 2016. X2 (EC 2700) has remained downstream.

Figure 4. Salinity at Jersey Point in early summer 2016. X2 (EC 2700) has remained downstream.

Figure 5. Tidally filtered flow at Jersey Point in early summer 2016. High negative flows are caused by South Delta exports during spring tides.

Figure 5. Tidally filtered flow at Jersey Point in early summer 2016. High negative flows are caused by South Delta exports during spring tides.