Category Archives: Bay-Delta

Smelt Update – April 1, 2016

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Since the last update, Delta and longfin smelt have continued their trends of record low numbers, as shown in the most recent Smelt Larvae Survey and 20-mm Survey. They are not yet gone, but close. It remains to be seen whether the good conditions provided so far in this wet winter 2016 can lead to some form of recovery for these two endangered species.

Longfin Smelt

With the high winter flows, the young from this year’s spawn are now distributed well to the west, although some remain in the north Delta (Figure 1). Their numbers continue at record low levels (Figure 2) despite a wet winter.

Figure 1. Longfin smelt catch in mid-March in Survey #1 of 20-mm Survey.

Figure 1. Longfin smelt catch in mid-March in Survey #1 of 20-mm Survey.

Figure 2. Average catch-per-unit-effort of young longfin smelt in mid-March 20-mm surveys from 2008-2016.

Figure 2. Average catch-per-unit-effort of young longfin smelt in mid-March 20-mm surveys from 2008-2016.

Delta Smelt

Delta smelt have yet to grow into the size range captured in the 20-mm Survey, but remain present in the last Smelt Larvae Survey (Figure 3). High winter through-Delta flows have resulted in a slightly more westward distribution than in recent drought years such as 2013 (Figure 4). Although numbers collected are very low, it is too early to determine relative production for 2016 compared to previous years in the Smelt Larvae Survey or the 20-mm Survey. Under similar wet winter-spring conditions in 2010 and 2011, Delta smelt had modest population improvements. It remains to be seen if the very low adult spawning population this year (in comparison to the populations in 2010 and 2011) can lead to some form of recovery in the population under this year’s relatively wet conditions.

Figure 3. Delta smelt larvae catch distribution in mid-March 2016 Smelt Larvae Survey.

Figure 3. Delta smelt larvae catch distribution in mid-March 2016 Smelt Larvae Survey.

Figure 4. Delta smelt larvae catch distribution in mid-March 2013 Smelt Larvae Survey.

Figure 4. Delta smelt larvae catch distribution in mid-March 2013 Smelt Larvae Survey.

Feinstein Gets Some Water, but Smelt Get Some Back

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In my March 12 post, I related that Senator Feinstein’s request for higher Delta exports would put the Delta Smelt population in the Delta at further risk of extinction. Well, she received her wish, and exports increased from 6000 cfs to 8000 cfs (11,400 cfs is maximum pumping capacity) in the week after her request when storms brought more inflow to Delta from the San Joaquin River.

However, the higher exports were short–lived, because the 3/14-3/17 Smelt Larvae Survey picked up larval smelt for the first time this year (Figure 1 – green dots). Exports dropped below 5000 cfs again. Though only two newly hatched larvae were collected in the central Delta, their presence is a concern. The presence of larval smelt shows that smelt are spawning in the lower San Joaquin River in the central Delta. According to the Smelt Working Group the net negative flows shown in red in Figure 1 for late March indicate a “medium” risk to smelt and a likelihood that larval smelt will be drawn toward the south Delta export pumps.1 The -5000 cfs Old and Middle River (OMR) reverse flows are the maximum allowed under the Smelt Biological Opinion.

In its review of the results of particle tracking model runs, the Smelt Working Group concluded: “Members stressed the importance of weighing more heavily the results from inserting (particles) at Prisoner’s Point, given the consistent catch of adults there this year and the hydrologic proximity of that location to the south Delta (as compared to Jersey Point). For OMR flow of -5000 cfs, approximately 20% of the particles inserted at Prisoners Point were entrained into the South Delta. For an OMR flow of -2500 cfs, approximately 10% of particles inserted at Prisoners Point were entrained into the South Delta. For an OMR flow of – 1250 cfs, less than 10% of particles inserted at Prisoners Point were entrained into the South Delta.” Prisoners Point is the green dot from the right on the Figure 1 map. In all likelihood, larval smelt are now being drawn or will soon be drawn into the south Delta. It is too early to determine what portion of the population is subject to this risk. But given the unprecedented depressed condition of the smelt population after four years of drought, the risk is significant.

On March 24, after review of “Smelt Working Group’s March 21 recommendations,2 the U.S. Fish and Wildlife Service “determined”3 that the OMR should be no more negative than -2500 cfs on a 14-day average, and no more negative than -3150 cfs on a five-day average. Reclamation took a slightly more liberal interpretation in the subsequent week’s operations (Figure 2), staying nearer -3500 cfs most of the week with no apparent interest in reaching a -2500 cfs 14-day average. It could be that the Service meant to recommend a -3500 cfs OMR limit. Or maybe the Service got a call from Senator Feinstein’s office. We shall see what this week’s meetings and determinations offer.

In any event, the risk to Delta Smelt remains “medium” at combined exports of about 3500-4000 cfs. With an export capacity of 11,400 cfs, Delta outflow still exceeding 50,000 cfs, reservoirs continuing to release snowmelt, and San Luis Reservoir in the San Joaquin Valley only half full, there will be continued cry for more exports and for approval of the Tunnels. In the meantime, it appears from Figure 1 that some smelt larvae and a good amount of snowmelt are escaping west to Suisun Bay, while some larval smelt remain at risk in the central Delta.

Figure 1. Net daily flow in Delta in late-March 2016. (Gage data source: USGS). Green dots are location of seven Delta Smelt larvae collected in Survey 6 of Smelt Larvae Survey (http://www.dfg.ca.gov/delta/data/sls/CPUE_Map.asp ).

Figure 1. Net daily flow in Delta in late-March 2016. (Gage data source: USGS). Green dots are location of seven Delta Smelt larvae collected in Survey 6 of Smelt Larvae Survey (http://www.dfg.ca.gov/delta/data/sls/CPUE_Map.asp ).

Figure 2. OMR March 23 to March 28. (Source: CDEC)

Figure 2. OMR March 23 to March 28. (Source: CDEC)

Fremont Weir Overflows Again – Prepare for Salmon and Sturgeon Rescues

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fish rescuesIt is one of those wet springs when the Sacramento River has spilled over the Fremont Weir at the upstream (north) entrance to the Yolo Bypass near Verona. In a January post I summarized the need to fix salmon and sturgeon passage at the weir. In early April 2011 adult sturgeon and salmon were rescued at Tisdale and Fremont weirs1 under nearly the same circumstances that have developed since mid-March this year. In the coming weeks, many adult sturgeon and Winter Run salmon attracted by the high Bypass flows will again show up and become stranded at the Fremont Weir as the weir ceases to overflow. River levels are expected to drop as much as eight feet in the coming week. As the Bypass slowly drains in the coming days more and more salmon and sturgeon will migrate up the Bypass via Cache Slough near Rio Vista. Many will become stranded in the upper Bypass as far up as the Fremont Weir concrete apron, where rescues occurred in the past.

map of flowsOthers will make their way to the west side of the upper Bypass to outlet of the Knights Landing Ridge Cut (KLRC), and migrate up into the Colusa Basin via the Colusa Basin Drain where they will be lost. In spring 2013, many Winter Run salmon were found stranded in the Colusa Basin under similar circumstances. The peak migration of Winter Run and sturgeon is in March and April. So I expect many salmon have or will be headed up the Ridge Cut, which is flowing 500-600 cfs.2 The CDFW trap is removed from the Ridge Cut outlet at such high flows.

Fixes for both problems are in the works, as they are required in the Central Valley Salmon Biological Opinion for operating the state and federal water projects. Reclamation District 108 is working on the outlet solution for the KLRC. DWR, DFW, and others are working on Fremont Weir passage. 3

In the meantime, trapping and rescues are the only measures to save fish again this year. These efforts should start soon. Note similar problems occur at the Moulton, Colusa, and Tisdale weirs (see map and last photo).

Above Photo: Fremont Weir on March 13, 2016. Overflow to Yolo Bypass was 30,000-40,000 cfs. Overflow peaked at 65,000 cfs two days later, as river stage rose to 36 ft, two feet above that in photo. For video of overflow event and Bypass flooding see http://youtu.be/9hrn2bSgg8A .

Above Photo: Fremont Weir on March 13, 2016. Overflow to Yolo Bypass was 30,000-40,000 cfs. Overflow peaked at 65,000 cfs two days later, as river stage rose to 36 ft, two feet above that in photo. For video of overflow event and Bypass flooding see http://youtu.be/9hrn2bSgg8A .

Above Photo: Fremont Weir on March 20, 2016 when overflow temporarily ceased at river stage dropped to 33.5 ft. Insert: 2011 rescue photo.

Above Photo: Fremont Weir on March 20, 2016 when overflow temporarily ceased at river stage dropped to 33.5 ft. Insert: 2011 rescue photo.

Above photo: Moulton Weir in January 1997.

Above photo: Moulton Weir in January 1997.

Winter Run Salmon have taken the Brunt of Punishment from Reclamation’s Shasta-Trinity Drought Operations – what about 2016?

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In the last two summers, Winter Run salmon production was greatly reduced by Reclamation’s operations of the Shasta-Trinity Division of the Central Valley Project. While the drought brought on the problem and the specific damaging project operations, the damage done was in large part unnecessary. Furthermore, not all the blame should go to Reclamation – the State Water Board and resource agencies who condoned the damaging operations also deserve some of the dis-credit.

I wrote on the subject in some detail in November.1 Resource and management agencies who were responsible for the failure of two year classes of Winter Run continue to blame the drought or demands of water contractors on Shasta-Trinity storage (Figure 1). Soon they will prepare a plan for the coming irrigation season. The plan will depend greatly on present and coming late-winter weather and hydrology. Given that Shasta Reservoir likely will fill this spring, the plan will likely revert to operations similar to those of 2011 and 2012, the last two years when the reservoir filled.

NMFS graphic

Figure 1. NMFS blames the drought.

State Board’s Thoughts

The State Board has been thinking carefully about what to do this summer for Winter Run salmon. 2

  • “With the loss of two out of three cohorts of endangered wild winter-run Chinook salmon (2014 and 2015), it is critical that we develop cold water pool resources in the winter and spring to support temperature management needed later in the year for this third wild winter run Chinook salmon year class.” Comment: irrigation deliveries to Sacramento River Settlement Contractors in April and May of the last two years were a major cause of the loss of the cold-water pool in Shasta. This in turn led to high egg mortality in the upper Sacramento River just below Shasta. While cutting the April and May deliveries would have alleviated the greater part of the problem in both years, it is not all of the problem or solution. Operational changes in the Shasta-Trinity Division could have eliminated many of the problems with little impact to irrigation deliveries, at least in 2015.
  • “These data reflect a 97.9% mortality of winter-run Chinook salmon eggs and fry on the upper Sacramento River in 2015.” Comment: Yes, the excessive water temperatures allowed by the State Board by relaxing their water quality standards caused the nearly complete loss of 2015 Winter Run production.
  • “Shasta operations: Implementation and Exception Procedures for End of September (EOS) Storage of 1.9 MAF or below – As per RPA Action I.2.2.C, if the EOS storage is at or below 1.9 MAF, then Keswick releases shall be managed to improve storage and maintained at 3,250 cfs unless hydrology improves.” Comment: Hydrology in the Central Valley has greatly improved with El Niño, yet releases were kept at 3250 cfs all winter, to the further detriment of the Winter Run, and were only increased well after Shasta exceeded the reservoir level at which Reclamation is supposed to release water to protect against floods. Young salmon need flow pulses to successfully migrate downstream from spawning and rearing areas.
  • “Given the substantial mortality of Sacramento River winter-run Chinook during the egg incubation and emergence periods in BYs 2014 and 2015, there is a need to conservatively manage for protection of the third of three winter-run Chinook cohorts, which will return to spawn upper Sacramento River beginning in summer of 2016. In the coming months, Reclamation and NMFS will be evaluating different actions to balance fishery needs, water supply, and water quality to develop a greater likelihood of protecting juvenile winter-run from BY 2016. As mentioned previously, any proposed action will require the cooperation of senior water rights holders on the Sacramento River and a system-wide operational approach to prioritize cold-water storage and operations at Shasta Lake.” Comment: After the failures in 2014 and 2015, we await the final plan for 2016.
  • “Under any hydrologic exceedence scenarios, there is a need to maximize water storage in Lake Shasta to comply with the December 15, 2015 adopted Order and also increase the likelihood of successfully implementing a water temperature management plan to benefit winter run Chinook salmon. The NMFS has prepared some initial concepts to achieve storage and temperature goals (Attachment 4) (Figure 2). In general, the proposed concept involves flow release as low as 2750 and 3250 until late May or initiation of a water temperature management plan.” Comment: The suggested NMFS improvements (“2016 adjustment”) would be a great benefit, particularly the 53°F DAT (daily average temperature) at Clear Creek in Redding (CCR). Obviously, 53°F would be a substantial improvement over last year’s allowed 58°F. The change is reasonably conservative given the present state of the population. The 55°F 7-day average daily maximum option leaves too much room for error, such as a day of lethal temperatures. Given the circumstances, we can only hope that NMFS recommends the more conservative approach, as it will also greatly help downstream habitat conditions at Balls Ferry and Jellys Ferry, which would further benefit Winter Run.
NMFS temp criteria...

Figure 2. NMFS considerations for the coming summer water temperature standard in the Sacramento River near Redding.

Present Prognosis

Nearly half way through the water year it is safe to say there is a very reasonable chance there will be adequate water resources to save the Winter Run salmon this year. Shasta storage is sharply rising (Figure 3). The reservoir will likely fill this spring for the first time since 2012. The snow pack is also above average.

Graph of Shasta Storage 2010-16

Figure 3. Shasta Reservoir storage water years 2011-2015. (Data source: CDEC)

Recommendations

Reasonable water temperature criteria for 2016 are:

  1. Maximum daily average water temperature in Keswick Reservoir release – 53F.
  2. Maximum daily average water temperature at Red Bluff – 58F.

Both these criteria were achieved in 2011 and 2012 (Figures 4 and 5), the last two years when Shasta Reservoir filled.

Graph of Red Bluff Temps 2011-13

Figure 4. Water temperature (daily average) in Sacramento River at Red Bluff – April 2011 to November 2013.

Graph of Keswick Temps 2011-13

Figure 5. Daily average water temperature of Keswick Reservoir release – April 2011 to March 2013.

More Information

For more information on saving the Winter Run Chinook Salmon in the Sacramento River and Delta see the following sources:

http://deltacouncil.ca.gov/2015-long-term-operations-biological-opinions-annual-science-review-review-materials-supplemental

http://www.westcoast.fisheries.noaa.gov/stories/2015/23_12232015_winter_chinook_math.html

http://mavensnotebook.com/2015/12/15/conserving-chinook-salmon-at-the-southern-end-of-their-range-challenges-and-opportunities/

http://www.westcoast.fisheries.noaa.gov/publications/Central_Valley/Water%20Operations/ Delta%20Operations%20for%20Salmonids%20and%20Sturgeon/ DOSS%20WY2016/2016.02.09_final_doss_notes.pdf

Largemouth Bass Production in the Delta

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I had the unique opportunity to study fish use of shallow inshore waters of the western Delta in 1978-79 and again in 2004-05. One of the biggest differences I noticed after 25 years was the increase in Largemouth Bass production. Mitigation areas where levees were breached allowing tides to enter-and-leave tidal ponds without flow-through were virtual Largemouth breeding factories. Areas where channel entrances had filled in and circulation reduced also were prone to aquatic plant proliferation and an abundance of non-native lake/pond fish including Largemouth, sunfish, and shiner minnows. Flow-through areas and tidal channels with two ends had lower Largemouth production (and more native fishes). Limited tidal circulation also caused prolific amounts of aquatic vegetation including water hyacinth, Egeria, milfoil, Parrots Feather, and Potamogeton. Dense beds of aquatic vegetation also occurred in bays, dead-end sloughs, breached islands, and protected shorelines.

A recent study1 relates higher Largemouth production to increases in aquatic plants, specifically relating the abundance of young Largemouth to Egeria. They also found young Largemouth more abundant in warmer waters, another feature of backwater areas. Aquatic plants slow currents, capture sediment, and absorb sunlight, which all contribute to warming of shallow waters.

One of the paper’s conclusions related to future habitat restoration:

“While these efforts will expand the largely missing shallow-water habitat in the Delta, a major concern is that increased shallow water area will expand the habitat for Brazilian waterweed and consequently increase the abundance of Largemouth Bass, creating a predation sink for target native fishes (Brown 2003).”

I have some points of disagreement with these conclusions. First, I do not believe the Delta lacks shallow water habitat. The problem, rather, is that too much of existing shallow water habitat is bad habitat more conducive to non-native warm water fish. Second, good shallow habitat along the edges of the bays and rivers has been and continues being lost to riprapping, ship-channel dredging, remnant soft-levee erosion, and filling with sediment.

I concur with the paper that much planned restoration will create more bad habitat. Instead we should be protecting good habitat and converting more of the bad habitat to good habitat.

For more on the subject of Delta habitat restoration see: http://calsport.org/news/cspas-assessment-of-historical-habitat-restoration-in-the-delta/ .