Category Archives: Fish (general)

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.

Longfin Smelt are Really Nearly Gone

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In previous posts, I described the poor status of longfin smelt in the Bay-Delta estuary.  In my last longfin post in April, I recommended a higher prescribed June Delta outflow, but none occurred.  June outflow was a bare minimum daily 7000 cfs.  As it turns out, it may not have done much good because there were simply too few spawners available this year (Figure 1).  The Fall Midwater Trawl Index (Recruits) was at a record low as in 2015.  The spawner indices for 2017 and 2018 will be less than 0.6, which is so low that few if any recruits will be produced.

Figure 1. Longfin Recruits (Fall Midwater Trawl Index) vs Spawners (Index from two years prior) in Log10 scale. The relationship is very strong and highly statistically significant. Taking into account Delta outflow in winter-spring makes the relationship even stronger. Recruits per spawner are dramatically lower in drier, low-outflow years (red years). The low recruitment in 2015 and 2016 does not bode well for future recruits in 2017 and 2018: it is likely that the values will be closer to 0/0.

Figure 1. Longfin Recruits (Fall Midwater Trawl Index) vs Spawners (Index from two years prior) in Log10 scale. The relationship is very strong and highly statistically significant. Taking into account Delta outflow in winter-spring makes the relationship even stronger. Recruits per spawner are dramatically lower in drier, low-outflow years (red years). The low recruitment in 2015 and 2016 does not bode well for future recruits in 2017 and 2018: it is likely that the values will be closer to 0/0.

Feinstein’s “Poison Pill” for Salmon and Smelt

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Senator Feinstein has added a rider to the Drought Water Bill that has been referred to as a “poison pill” for endangered salmon and smelt. Senator Boxer has vowed to fight passage of the Water Bill because of Feinstein’s “poison pill” rider. Senator Feinstein has claimed that the rider is a compromise to get support for the overall water bill that includes provisions to enhance California’s water supply infrastructure.

“Even amid heavy storms, only 852,000 of the 5.5 million acre-feet of water that flowed into the Delta during the first two months of this year—enough to sustain nearly two million acres of farm land—was sent south. The rest drained into the San Francisco Bay due to a lack of surface storage in the Sierras and pumping restrictions ostensibly intended to protect endangered species…. The Feinstein rider would give regulators some discretion to increase pumping to a little less than half of capacity.” Wall Street Journal article.

Senator Feinstein’s rider would allow weakening of provisions in the federal salmon and smelt biological opinions that restrict Delta export pumping from December to June (Figure 1). The rider would allow more Delta export pumping during periods of higher Delta outflow, as in the two storm periods shown in Figure 1 (bottom chart). Even if this weakening only allowed increased exports up to 50% of capacity, exports could be raised to approximately 13,000 acre-ft per day from the present 2500 to 10,000 acre-feet per day limits under the biological opinions (the amounts vary with the immediate risk to species). These risks would be substantial and would further jeopardize winter-run salmon, spring-run salmon, green sturgeon, steelhead, Delta smelt, and longfin smelt. All of these species depend heavily on the Bay-Delta during the times of year in which the current biological opinions potentially restrict exports.

Figure 1. Delta export pumping (top) and Delta outflow (bottom) in Water Year 2016.

Figure 1. Delta export pumping (top) and Delta outflow (bottom) in Water Year 2016.

Obsession with Fall X2

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There is a science-management obsession with Fall X2 – the location of the 2 parts-per-thousand salinity location in the Bay-Delta in the autumn.  More specifically, Fall X2 is the average km location of X2 for the months of September-December.  Such an average index seems ridiculous given that X2 varies so much especially in December, or even in a year like 2016 in October-November.  Despite this, resource agencies have been intent on trying to manage the Delta smelt population by manipulating Fall X2 based on the relationship between Fall X2 and the following spring 20-mm survey smelt index shown in Figure 1.  Fall X2 is an element of Action 4 in the Smelt OCAP Biological Opinion.

Figure 1. Fall X2 versus 20-mm Survey Delta smelt index.

Figure 1. Fall X2 versus 20-mm Survey Delta smelt index.

The problem is not that fall flows and X2 location are not important to Delta smelt. It’s that the previous year’s winter-through-fall flows, Delta exports, and fall adult population abundance are all related to the subsequent year’s production of smelt. So are winter-spring conditions. Smelt production in any year is related to all these factors, with some factors being more important in some years. A spring index can be low for many reasons, including bad conditions that spring regardless of the location of X2 the previous fall.

Focusing on any one parameter like Fall X2 is dangerous. Since there is only limited water in a drought year, it is critical that available water be distributed in a way it does the most good. If all the smelt die in June, it doesn’t help much to allocate a lot of water in the fall.

Figure 2. River kilometer reference locations for X2. Collinsville (km 81), Mallard Island, and Port Chicago are standard reference locations when specifying X2 standards.

Figure 2. River kilometer reference locations for X2. Collinsville (km 81), Mallard Island, and Port Chicago are standard reference locations when specifying X2 standards.

The Fall X2 factor is being studied in the FLaSH program.1 The study is being undertaken as an adaptive management experiment. “According to the FLaSH conceptual model, conditions are supposed to be favorable for Delta Smelt when fall X2 is approximately 74 km or less, unfavorable when X2 is approximately 85 km or greater, and intermediate in between (Reclamation 2011, 2012). Surface area for the LSZ at X2s of 74 km and 85 km were predicted to be 4000 and 9000 hectares, respectively (Reclamation 2011, 2012).”

The Smelt BO is being revised by the US Fish and Wildlife Service. The State Board is considering new Delta water quality standards for the Delta. Let’s hope they place less emphasis on the Fall X2 factor and more emphasis on progressively managing hydrology, water quality, and fish populations in the Bay-Delta.

Winter-Run Salmon Emigration and First Fall-Winter Rains

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In a recent post I discussed the importance of the first fall rains in stimulating the emigration of juvenile winter-run Chinook salmon from the Redding/RedBluff spawning and rearing area of the Sacramento River below Shasta Dam.

Juvenile salmon trap and seine data from fall and early winter of 2015 and 2016 further support the importance of these first-of-season rains to the emigration of winter-run salmon emigration to the Delta, Bay, and ocean. The pertinent data were obtained from trap and seine collections from four locations (Red Bluff, Tisdale-Wilkins, Knights Landing, and Sacramento) shown in Figure 1.

This year’s (2016) fall migration pattern (Figure 2) shows the marked uptick in movement (catch) with the late October storms. Movement had begun gradually in early September from Red Bluff to Tisdale Weir, with some fish showing up at Sacramento. Most of the fish located above Sacramento seemed to take advantage of the storm-water surge, since the plots for the cumulative capture of juvenile salmon at the Red Bluff, Tisdale Weir, and Knights Landing locations flattened off after the storms.

The previous year’s (2015) migration pattern (Figure 3) indicates that the fish waited until the first storms at the end of fall and beginning of winter before moving from the river into the Delta at Sacramento. The March movements indicated in Sacramento and Chipps Island (entrance to SF Bay) trawl catches are indicative of February-March stocking of hatchery smolts near Redding – these larger smolts are not readily detected in river screw traps and seines.

A recent study report1 describes how low flows result in “long in-river residence and low survival whereas strong peak flows corresponded to rapid emigration and high survival… Overall, this study highlights the importance of pulsed flow conditions for promoting higher survival of juvenile Winter-Run Chinook Salmon emigrating to the ocean.” The study notes that survival is proportional to the cumulative catch. Note that the catch in 2016 is nearly 50% higher so far than it was in 2015.

The recent data confirms the need to bypass some of the inflow to Central Valley rim dams during early storm pulses. This bypass of flow to spawning and rearing areas just downstream of the dams gets salmon moving downstream. It is equally important to limit Delta exports during these peak juvenile emigration periods. Success during storm events is critical for endangered salmon to reach the Bay and ocean.

Figure 1. Location of four trap and seine locations in Sacramento River between Red Bluff (river mile 243) and Sacramento (river-mile 54).

Figure 1. Location of four trap and seine locations in Sacramento River between Red Bluff (river mile 243) and Sacramento (river-mile 54).

Figure 2. Winter-run Chinook salmon cumulative catch at Sacramento River collection sites in fall 2016 plus river flow at Wilkins Slough gage (CDEC data).

Figure 2. Winter-run Chinook salmon cumulative catch at Sacramento River collection sites in fall 2016 (www.cbr.washington.edu/sacramento), plus river flow at Wilkins Slough gage (CDEC data).

Figure 3. Winter-run Chinook salmon cumulative catch at Sacramento River collection sites in fall-winter 2015 (www.cbr.washington.edu/sacramento), plus river flow at Wilkins Slough gage (CDEC data)

Figure 3. Winter-run Chinook salmon cumulative catch at Sacramento River collection sites in fall-winter 2015 (www.cbr.washington.edu/sacramento), plus river flow at Wilkins Slough gage (CDEC data)

  1. http://scienceconf2016.deltacouncil.ca.gov/sites/default/files/2016-11-02-Accepted-Poster-Abstracts.pdf. Emigration Rate and Survival of Winter-run Chinook Salmon. Jason Hassrick, ICF International, jason.hassrick@icfi.com. Arnold Ammann, NOAA Southwest Fisheries Science Center, arnold.ammann@noaa.gov. p. 64. ↩