Category Archives: Smelt

Winter in the Delta – Salmon and Smelt

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December and January have traditionally been the months when salmon and smelt enter the Delta in large numbers with late fall and early winter storms. Juvenile and yearling salmon pour out of the rivers into the Delta. Heavy rains wash fry, parr, and smolts from their river spawning grounds into the Delta. Sub-yearling winter-run, yearling late-fall, spring-run, and fall-run, and newly hatched spring and fall-run fry abound. Adult longfin and Delta smelt migrate up from the Bay, surfing the tides on their annual spawning runs.

These same storms whet the appetite for December exports from the south Delta. In the two decades from 1990 to 2010, December and January exports often reached 11,000 cfs and at times exceeded 12,000 cfs. High salvage events occurred for salmon and smelt, reflecting both the abundance of fish and the strong pull of reverse flows toward the south Delta pumps. Precipitous population declines followed, forcing severe winter export limitations (only 1500-5000 cfs) imposed since 2008-2009 by ESA biological opinions to reduce fish losses. Winter salvage at the south Delta export facilities dropped sharply as a result of the limitations, but salmon and smelt populations had already reached record lows, and most remained so or got even worse during the 2012-2015 drought.

This year’s fall storms and high December Delta inflows has brought a new regulatory reality to Delta exports. The federal and state governments, under new mandates in the recently-passed federal water legislation, have kept exports high (9000-11,000 cfs) or moderate (5000-7000 cfs) through December, hoping fish would still be protected but allowing water supply deliveries to increase after four years of drought. South Delta salvage has remained relatively low so far, but there are signs of that potentially changing.

Smelt surveys indicate a small potential resurgence of the Delta smelt population and the presence of pre-spawning adult Delta smelt in the west and central Delta. The Smelt Working Group (SWG), state and federal biologists charged with advising water project managers, have recommended cutting exports to protect the smelt. Their concern stems not only from the risk of salvage at the pumps, but also from the fact that high exports may draw the smelt spawners into the central Delta where their offspring will be more susceptible to entrainment at the export pumps.

All the SWG risk factors appear to be in play in mid-December 2016 (Figure 1). Adult smelt have been captured in net surveys in the central Delta (yellow highlight). The turbidity front (>10 ntu) is approaching the south Delta. Old-and-Middle-River reverse flows (OMR) and exports are about -7000 cfs. Delta inflow and outflow are relatively high.

We will all be watching in the coming weeks to see whether what was billed as a “compromise” in the just-passed federal water legislation is protective of salmon and smelt.. If not, we will also be watching to see whether we are in the midst of an important adaptive management experiment that will adjust exports to protect fish, or whether federal managers will instead expect us to adapt our expectations and watch more fish die.

Figure 1. Mid-December 2016 Risk factors assessed by the Smelt Working Group in advising federal and state water project managers. Under these conditions, adult Delta smelt are apt to enter the central Delta as they have so far in mid-December 2016 (smelt distribution shown as yellow highlight). Direct risk to adult smelt will increase when the turbidity front reaches the export pumps.

Figure 1. Mid-December 2016 Risk factors assessed by the Smelt Working Group in advising federal and state water project managers. Under these conditions, adult Delta smelt are apt to enter the central Delta as they have so far in mid-December 2016 (smelt distribution shown as yellow highlight). Direct risk to adult smelt will increase when the turbidity front reaches the export pumps.

Smelt Conflict Continues

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The Smelt Working Group (SWG) again this week recommended major cutbacks in Delta exports (about a 75% cutback)1 to protect Delta smelt adults that entered the Delta this past month on their annual pre-spawning migration from the Bay. Managers from the US Fish and Wildlife Service (FWS), in taking formal action on the recommendation as they did in the prior week, did not adopt the recommendation. Instead FWS managers maintained a less restrictive regime that allows exports of at least 50% of capacity (5,600 cfs).2 A conflict arises in these circumstances because high Delta inflows from recent storms could be exported at maximum rates (11,200 cfs) to south-of-Delta storage (e.g., San Luis Reservoir) if the restrictions in the Delta Smelt Biological Opinion are not applied. In recent days, Reclamation and CDWR have kept Old and Middle River reverse flows (OMR) at about -6500 cfs (Figure 1) by holding exports at 7000 cfs, but they contemplate increasing exports “if conditions continue to settle following last week’s storm”. The reference to “settle” refers to an expected reduction in Delta turbidity, which has been related to the export entrainment risk to Delta smelt.

The “conflict” arises between what the SWG is recommending for 14 days – exports of about 2500 cfs – and what the FWS managers will allow (some amount greater than 7000 cfs). The FWS “does not believe that Action 1 is currently necessary in response to last week’s storm,” whereas the SWG believes action is needed based on the presence of adult smelt as far upstream as Prisoners Point in the San Joaquin channel. The SWG includes FWS smelt experts. The FWS, Reclamation, and DWR managers coordinate on the FWS’s “formal action”.

While the holidays will restrict SWG and FWS actions in the next two weeks, some monitoring will continue that could indicate the need for changes in Delta operations during this period. Of chief concern is potential salvage of smelt at the south Delta export facilities. Of note this week is sharply increased salvage of late fall/winter run salmon smolts from the Sacramento River. 3

smelt-confilict

  1. Biological Opinion : Action 1 of the RPA (- 2,000 cfs OMR for 14 days with a corresponding 5 day average OMR of -2,500 cfs. ↩
  2. Moderate exports are allowed in the new water bill signed by the President on 12/16. The target of -5000 cfs OMR flow in the central Delta under high Delta inflow can actually be met with up to 7000 cfs of exports. ↩
  3. https://www.usbr.gov/mp/cvo/vungvari/salmondly.pdf ↩

Another Chance for Delta Smelt – 2017 Comeback?

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In 2010 Delta smelt started a two-year comeback after three years of drought.  The fourth lowest fall index on record (2009) brought a modest increase in the normal water year 2010 summer and fall indices that in turn led to the modest 2011 wet year recovery.  Another comeback may be in the making with the wet fall-winter of water year 2017.  After the record low 2015 summer and fall indices, and what were perceived to be record lows in 2016, the remaining smelt seem to be making a run of it this wet fall-winter as they did in 2010 (Figures 1 and 2).  In 2010 exports were constrained by the 2009 Smelt Biological Opinion (BO) limits on OMR of -5000 cfs or below (Figure 3).  Only one Delta smelt was observed in December and January at the south Delta fish salvage facilities that year (most likely due to the export restrictions).  So far this year prescribed export restrictions and recommendations from the Smelt Working Group on OMR flows per the BO have been ignored, in part due to relaxations allowed in the new water bill the President signed last week.  Exports and negative OMR flows remain high (Figure 4).  With such high winter exports and associated highly negative OMR flows, it remains to be seen if salvage numbers remain low (none so far) and a comeback occurs in 2017.

Figure 1. Delta smelt distribution in January 2010 Kodiak Trawl Survey 2010. Source: CDFW.

Figure 1. Delta smelt distribution in January 2010 Kodiak Trawl Survey. Source: CDFW.

Figure 2. Delta smelt distribution in December 2016 Kodiak Trawl Survey. Source: CDFW.

Figure 2. Delta smelt distribution in December 2016 Kodiak Trawl Survey. Source: CDFW.

Figure 3. Old and Middle River net flow in the central Delta downstream of the South Delta export pumps 12/2/2009-1/28/2010. Negative flows are caused by reverse flows in these river channels toward the pumping facilities. Source: CDEC.

Figure 3. Old and Middle River net flow in the central Delta downstream of the South Delta export pumps 12/2/2009-1/28/2010. Negative flows are caused by reverse flows in these river channels toward the pumping facilities. Source: CDEC.

Figure 4. Old and Middle River net flow in the central Delta downstream of the South Delta export pumps 11/21/2016-12/21/2016. Negative flows are caused by reverse flows in these river channels toward the pumping facilities. Source: CDEC.

Figure 4. Old and Middle River net flow in the central Delta downstream of the South Delta export pumps 11/21/2016-12/21/2016. Negative flows are caused by reverse flows in these river channels toward the pumping facilities. Source: CDEC.

Smelt Working Group recommends cutting Delta exports when large group of Delta smelt shows in survey nets

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Last week I opined about the lack of agencies’ (Smelt Working Group) concern relating to high Delta exports so far this December.  SWG:  “However, members are concerned regarding today’s OMR flow (daily average of approximately -10,000 cfs) and how it could influence the future distribution of the species. … The SWG expressed concerns regarding the current OMR flow (~-10,000 cfs). … A minority of the membership stated that we do not know what percentage of the population is currently at risk of being entrained; that entrainment into the OMR corridor could be occurring now and we would not know it. This minority indicated OMR should not exceed -5,000 cfs immediately.”  (Smelt Working Group 12/5/16 meeting).

I was incorrect to label it a lack of concern when it was really lack of management action.  The SWG had noted that two smelt had been caught in November trawl surveys in the lower Sacramento River near X2 (~2700EC), which was above km 81 and below km 85 on 12/5 (X2 actually reached km 95 on high tides by 12/10/16).

Kilometers above the Golden Gate Bridge in Bay-Delta estuary.

Kilometers above the Golden Gate Bridge in Bay-Delta estuary.

As it turned out, the minority recommendation was not adopted and high exports (~10,000 cfs) continued.

On 12/12 the SWG met again.  It noted recent higher exports, an upstream movement of X2 to km 90 (because of higher exports), and perhaps most important the capture of 221 Delta smelt near km 90 in a single trawl on 12/10.  Three Delta smelt were also captured in a trawl in Three Mile Slough (km 98).  SWG:  “Members indicated great concern that Delta Smelt could begin migrating upstream in the very near future, and find appropriate cues to move upstream on the San Joaquin River and into the sphere of influence of the pumps where the adults and subsequent young of the year will be at increased risk of being entrained into the Old and Middle River corridors, or even into the facilities themselves.” 

At the 12/12 meeting, the SWG unanimously recommended reducing exports to limit OMR to -5000 cfs, per the Delta Smelt Biological Opinion.  Reclamation/Interior/CDWR management did not adopt this recommendation until 5 days later.  Exports were initially increased, and the OMR fell further to -10,323 cfs (see chart below) before export cutbacks started on 12/15, when the big surge of stormwater hit the Delta.  As a consequence of th surge, X2 on the lower San Joaquin River pushed downstream of km 90 after 12/17.  It is possible that some of the contingent of Delta smelt that were concentrated near X2 before 12/17 were drawn into the central Delta before OMR was limited.  It remains to be seen if the -5000 OMR limit will be adequate to protect what appears to be a potentially significant uptick in the Delta smelt spawning population compared to the past four years.  I wonder if these smelt were a consequence of last July’s outflow pulse.  Are Delta smelt potentially making a small comeback like water year 2010, when OMR December limits in the 2009 Delta smelt biological opinion were first put in place?

Combined flow in Old and Middle River in the central Delta. Minus flows represent the effects of Delta exports from the south Delta. Exports were cut from 11,000 cfs to 7500 cfs on 12/16-17.

Combined flow in Old and Middle River in the central Delta. Minus flows represent the effects of Delta exports from the south Delta. Exports were cut from 11,000 cfs to 7500 cfs on 12/16-17.

Salinity (EC) at Jersey Point in lower San Joaquin River (km 98) 12/9-12/17. Sharp drop after 12/14 due to reduced exports and higher Delta inflows.

Salinity (EC) at Jersey Point in lower San Joaquin River (km 98) 12/9-12/17. Sharp drop after 12/14 due to reduced exports and higher Delta inflows.

Federal Tracy Pumping Plant daily average exports from the south Delta 12/9-12/17. The Water Bill was signed by the President on 12/16, allowing increased federal Delta exports. (4400 max)

Federal Tracy Pumping Plant daily average exports from the south Delta 12/9-12/17. The Water Bill was signed by the President on 12/16, allowing increased federal Delta exports. (4400 max)

State Clifton Court daily average exports from the south Delta 12/9-12/17. (6800 max)

State Clifton Court daily average exports from the south Delta 12/9-12/17. (6800 max)

Have Agencies Given Up on Smelt and Salmon?

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Last winter I warned about DWR jumping the gun on December Delta exports before storm runoff hit the Delta (Whoa on the Delta Exports DWR). Well they have done it again. Knowing full well that this year’s few remaining smelt and winter -run salmon smolts are in or soon to be in the Delta, DWR has ratcheted up Delta exports several days before the anticipated storm runoff hits the Delta (Figure 1 and 2).

Figure 1. Delta inflow at Freeport 12/5-12/14, 2016. Source: CDEC.

Figure 1. Delta inflow at Freeport 12/5-12/14, 2016. Source: CDEC.

Figure 2. State Water Project daily average exports from Delta at Clifton Court Forebay 12/7-12/13, 2016. Maximum export rate for the State Water Project is 6676 cfs.

Figure 2. State Water Project daily average exports from Delta at Clifton Court Forebay 12/7-12/13, 2016. Maximum export rate for the State Water Project is 6676 cfs.

Their action has resulted in the movement of the Low Salinity Zone, X2, and brackish water upstream into the Delta. Old and Middle River (OMR) flows toward the south Delta export pumps have increased to their near maximum of -10,000 cfs (Figure 3), which draws brackish water from the Bay up into the Delta (Figure 4). The influx of brackish water is detrimental to water supply and fish habitat. Furthermore, high exports and negative OMR flows can draw juvenile salmon and adult smelt to the south Delta export pumps.

Constraints on OMR negative flows for winter-run salmon do not kick in until January. December limits on exports do not apply until salvage numbers of salmon rise. Salvage has not increased this year because the number of wild smolts produced is very low and hatchery smolts have yet to be released.

OMR constraints for Delta smelt should kick-in in December under present circumstances according to the Smelt Biological Opinion:

Low-entrainment risk period: delta smelt salvage has historically been low between December 1 and December 19, even during periods when first flush conditions (i.e., elevated river inflow and turbidity) occurred. During the low-entrainment risk period, the SWG shall determine if the information generated by physical (i.e. turbidity and river inflow) and biological (e.g., salvage, DFG trawls) monitoring indicates that delta smelt are vulnerable to entrainment or are likely to migrate into a region where future entrainment events may occur. If this occurs, the Service shall require initiation of Action 1 as described in Attachment B. Action 1 shall require the Projects to maintain OMR flows no more negative than -2,000 cfs (14-day average) with a simultaneous 5-day running average flow no more negative than -2,500 cfs to protect adult delta smelt for 14 days.

The Smelt Working Group met on December 5 and determined:

The Working Group reviewed present Delta conditions and observed a lack of recent data regarding species distribution. The Working Group did not make a recommendation for OMR flows The SWG will monitor hydrology conditions and ongoing surveys this week and will reconvene to for the protection of Delta Smelt adults. However, members are concerned regarding today’s OMR flow (daily average of approximately -10,000 cfs) and how it could influence the future distribution of the species. .. The SWG expressed concerns regarding the current OMR flow (~-10,000 cfs), but with the expected reduction later in the week to -7,000 to -8,000 cfs, influence of the pumps would be expected to decrease.

Note in Figure 3 that OMR went more negative than -8,000 cfs by December 13.

Since there are few if any Delta smelt remaining in the Bay-Delta, it will be difficult to assess risk. Given that the OMR had fallen below -9,000 cfs after the December 12 meeting because of near maximum south Delta exports, we can only assume those present at that meeting determined the assessed risk to be low. We can also assume that Interior and the state are no longer concerned with the fate of Delta smelt, as they obviously have not been able to find any in their early surveys.

Figure 3. Tidally filtered flows in Old and Middle Rivers in the south Delta. Increasingly negative flows are caused by increasing south Delta exports. South Delta exports were 10,800 cfs on Dec. 5.

Figure 3. Tidally filtered flows in Old and Middle Rivers in the south Delta. Increasingly negative flows are caused by increasing south Delta exports. South Delta exports were 10,800 cfs on Dec. 5.

Figure 4. Rising salinity in December 2016 at selected Delta locations. Blue dots are CDEC gage locations. Note freshwater reaching the two northern locations on or about Dec. 13.

Figure 4. Rising salinity in December 2016 at selected Delta locations. Blue dots are CDEC gage locations. Note freshwater reaching the two northern locations on or about Dec. 13.