Improved Yolo Bypass Fish Passage

Posted on May 10, 2019 by Tom Cannon

Some salmon and sturgeon adults migrating up the Sacramento River this spring have had new help in passing upstream via the Yolo Bypass. With roughly half the Sacramento River’s flood waters flowing through the Yolo Bypass at the beginning of March, many salmon and sturgeon returning to the upper river to spawn likely chose entered the lower end of the Bypass at Rio Vista. These fish had a new notch opening to help them get over the Fremont Weir at the upper end of the 40-mile-long Bypass (Figure 1) and back into the Sacramento River to continue their journey.

The new $6-million gated-notch opening in the Fremont Weir is the first of several to be built into the two-mile-wide weir to help fish passage. The notches will allow an easier passage route over the weir, especially for large sturgeon. The notches are especially important in allowing an extended period for adult fish to finish their passage through the Bypass when Sacramento River water levels fall and the river flow ceases spilling over the weir into the Bypass. In the past, these conditions would have trapped any fish that remained in the Bypass. The notches will also help pass downstream-migrating juvenile salmon to enter the Yolo Bypass, where there is potential beneficial tidal and floodplain rearing habitat.

The first year of the new notch’s operation has not been without some glitches.¹ Significant numbers of salmon and sturgeon have died and probably continue to die at the weir and in the Bypass.

But the new notch was not the underlying cause of this problem. The problem lies in flood control and reservoir storage management in the Central Valley. Drastic reductions in river flow and water levels led to fish stranding in the Bypass, the draining of the floodplain, and a rapid rise in water temperatures in the Bypass that stressed migrating fish.

Shasta/Keswick reservoir releases were reduced sharply after two major flood releases this winter/spring (Figure 2).
This led to abrupt ends to Fremont Weir overflows into the Yolo Bypass (Figure 3)
The sharp drops in water levels in the river allowed only one week of extended Bypass inflows through the new notch (Figure 4).
That led to a rapid draining of the Bypass (Figures 5 and 6).
This in turn led to excessive water temperatures in the Bypass (Figure 7) for migrating and rearing salmon (>70^oF).

For the new notches to be effective, an extended period of flow through the new notches will be needed to allow time for migrating and rearing salmon and sturgeon to safely exit the Yolo Bypass without being subjected to a sudden draining of warm water from the shallow margins of the Bypass. With a near record snowpack and filling reservoirs, there were sufficient river flows and reservoir storage this year to extend the duration of river flows into the Yolo Bypass.

Figure 1. New Fremont Weir gated notch to help fish passage between Yolo Bypass and Sacramento River.

Figure 2. Reservoir releases from Shasta/Keswick dams in winter-spring 2019.

Figure 3. Flow into Yolo Bypass from Sacramento River at Fremont Weir in winter-spring 2019.

Figure 4. Water elevation of Sacramento River at Fremont Weir in winter-spring 2019. Top of weir is at 32-ft elevation. Bottom of new notch is at 25-ft elevation. Extended operation of new notch would have occurred from April 22-28.

Figure 5. Flow in upper Yolo Bypass in winter-spring 2019.

Figure 6. Water elevation in mid Yolo Bypass during Bypass draining in last week of April 2019.

Figure 7. Water temperature in mid Yolo Bypass at Lisbon Weir during Bypass draining in last week of April 2019.

https://www.dailydemocrat.com/2019/05/01/fish-reported-to-be-using-fremont-weir-again/
https://www.sacbee.com/news/state/california/water-and-drought/delta/article229592929.html ↩

Shasta River Update – April 2019

Posted on April 6, 2019 by Tom Cannon

A February 20, 2019 article in the Eureka Times-Standard reported continuing improvement of Klamath River fall-run Chinook.

“The number of natural area spawners was 53,624 adults, which exceeded the preseason expectation of 40,700. However, the stock is still in “overfished” status as escapement was not met the previous three seasons. The estimated hatchery return was 18,564 adults for the basin.

Spawning escapement to the upper Klamath River tributaries (Salmon, Scott, and Shasta Rivers), where spawning was only minimally affected by hatchery strays, totaled 21,109 adults. The Shasta River has historically been the most important Chinook salmon spawning stream in the upper Klamath River, supporting a spawning escapement of 27,600 adults as recently as 2012 and 63,700 in 1935. The escapement in 2018 to the Shasta River was 18,673 adults. Escapement to the Salmon and Scott Rivers was 1,228 and 1,208 adults, respectively.”

In a May 2017 post, I discussed an increasing contribution to the Klamath run from the Shasta River. In Figure 1 below, I have updated my original spawner-recruit analysis from the prior post with 2017 and 2018 escapement numbers for the Shasta River. The Shasta run in fall 2018 was third highest on record for the Shasta River. The river’s fall-run population continues to benefit from improved water management. Coho salmon and steelhead have yet to show significant improvements (Figure 2).

An February 26, 2019 article from the publication Grist (posted in 2/26/19 Maven’s Digest) describes changes to water management in the Shasta River. The Nature Conservancy, using public grant funds, purchased the nearly 5000-acre Shasta Big Springs Ranch for $14 million in 2009. More recently, the California Department of Fish and Wildlife purchased the water rights of the Shasta Big Springs Ranch. Now, more water is left in the Shasta River, and only a third (1500 acres) of the ranch remains irrigated. The article in Grist states that the new allocation of water has negatively affected the ranch’s ability to support wildlife and threatened its ability to support ranching. In addition, the article questions the benefits of the new management regime to fish: “[T]he fish don’t seem to be doing much better either.”

While some will argue the relative values of ranching and fish protection, I see no grounds to argue that changes in water management have not been positive to the Shasta River and Klamath River salmon. Summer flows in the river below the ranch appear to have improved over the long term average (Figure 3). Many of the Shasta River’s Chinook and Coho salmon spawn in the Big Springs area and in the river below Big Springs, and depend on flow and cold water input from the springs. Even with the contribution of this flow, water temperatures are marginal (>65^oF) for young salmon from May to September (Figure 4).

From my perspective, the loss of several thousand acres of irrigated pasture out of roughly 25,000 acres in the Shasta Valley seems a small price to pay for a large step towards the recovery of Shasta and Klamath River salmon.

Figure 1. Spawner-recruit relationship for Shasta River. Escapement estimates (log10X – 2 transformed) are plotted for recruits by escapement (spawners) three years earlier. Year shown is recruit (escapement) year. The number is the year that fish returned to the Shasta River to spawn. The color of the number depicts the water-year type in the Shasta River during the year the recruits reared. The color of the circle depicts the water-year type in the Klamath River during the year the recruits reared. Blue is for Wet water-year types. Green is for Normal water-year types. Red is for Dry water-year types. Example: 90 depicts fish that returned to the Shasta River as adult spawners in 1990. These fish were spawned in 1987 and reared in winter-spring 1988. The red number shows that the 1988 rearing year was a Dry water year in the Shasta River; the red circle shows that the 1988 rearing year was a Dry water year in the Klamath River. Note very poor recruits per spawner in 1990-1993 drought period, compared with relatively high recruits per spawner from 2011-2018, even though the latter period included the 2012-2016 drought.

Figure 2. Shasta River salmonid runs from 1930 to 2017. Source: https://www.casalmon.org/salmon-snapshots/history/shasta-river

Figure 3. Shasta River flows in the Shasta River below Big Springs 2016-2018 with 30 year average. Note summer base flow appears to have improved by approximately 10-30 cfs.

Figure 4. Water temperature in the Shasta River below Big Springs including summers of 2017 and 2018. Source: DWR CDEC.

Revised Delta Smelt Take Permit

Posted on March 25, 2019 by Tom Cannon

The Interior Department’s US Fish and Wildlife Service (USFWS) issued a memo¹ on January 30, 2019 that revised the federal take permit for Delta smelt for the combined operation of the Central Valley Project and the State Water Project. The memo stated:

“It has become clear over the past several years that surveys are reaching their detection limits given the declining population of delta smelt, and in 2018, the FMWT [fall midwater trawl] Index was zero, indicating that the FMWT Index may no longer provide an accurate predictor of incidental take.”

The new take criteria are now the old action criteria of limiting Old and Middle River (OMR) reverse flows during the winter and spring under certain conditions. When smelt would normally be expected to be present, OMR flows would be restricted to being no more negative than -2000 or -5000 cfs. The new “surrogate” criteria essentially keep the south Delta pumping plant operations at status quo until such time as the ongoing reinitiated Endangered Species Act (ESA) consultation is completed and new take permits are issued.

The importance of the rule change is diminished by the fact that Interior (combined action of US Bureau of Reclamation and USFWS) has not enforced the rules to protect Delta smelt. The state of California has also failed to protect Delta smelt as well as California ESA-listed longfin smelt. One only has to review recent early winter information to see this is the case. After the first Delta outflow pulse at the beginning of December 2018, outflow fell to only 4000 through mid-December (Figure 1). High exports (Figure 2) contributed to the low outflow and exceptionally low (negative) OMR flows (Figure 3).

These low outflows and high exports created very high risk conditions for the two smelt species. What few Delta smelt remained were observed in the west Delta (Figure 4). Longfin smelt were spawning in Suisun Bay and the west Delta (Figures 5 and 6).

Smelt are not being protected. The Smelt Working Group mandated under the Federal and State take permits has been inactive and has not provided mandatory guidance. New take permits are needed immediately to protect the two listed smelts. The State Water Board, in revisiting water right permits and water quality standards for the Delta, should also adequately protect the listed smelts. To protect the smelts, the OMR limit for December should have been no more negative than -2000 cfs. The export-to-inflow limit criteria for December should be 35%, not the present 65%. December outflow minimums should be 6000-8000 cfs, not the present 3500-4500 cfs.

Figure 1. Delta outflow 11/10/18 to 1/8/19. Note very low outflow in early December after initial rainfall pulse.

Figure 2. State project exports at Clifton Court December 2018 to February 2019. Federal exports were near maximum (3500-4200 cfs) for most of period.

Figure 3. OMR flows November 2018 to January 2019.

Figure 4. December 2018 Kodiak trawl survey catch of Delta smelt.

Figure 5. December 2018 midwater trawl longfin smelt catch.

Figure 6. Smelt Larvae Survey #1 for 2019 catch of newly hatched longfin smelt.

https://www.fws.gov/sfbaydelta/CVP-SWP/documents/2008Biop_ITS_01302019_signed.pdf ↩

Longfin Smelt End of 2018 A Case for Higher Delta Outflow Standards in June

Posted on January 9, 2019 by Tom Cannon

In a February 2018 post I last updated the status of longfin smelt in the Bay-Delta. I showed that longfin smelt have a strong spawner-recruit or stock-recruitment relationship wherein new recruits into the population depend on the abundance of spawning parents (Figure 1). The relationship also indicated a strong influence of water–year type.

What is it in wetter years that improves survival? What is it about wet years that is important to longfin survival? My analysis is it is the spring Delta outflow, with June likely being important. The fall longfin index is significantly correlated with June outflow (Figure 2). It requires Delta outflows in the 8000-10,000 cfs range to keep the low salinity zone and young longfin in the Bay, west of the Delta and away from the south Delta export pumps and warm low-productivity pelagic habitats.

Present standards (see link, pdf pages 26-27) for June require outflow of 7100 cfs on a 30-day running average. This contrasts sharply with previous June standards under Water Rights Decision 1485 (see link, pdf page 43) which required an average monthly flow of 9500 cfs in some below normal years, 10,700 cfs in Above Normal years, and 14,000 cfs in Wet years. In its ongoing update of the Bay-Delta Plan, the State Water Resources Control Board must account for the importance of the outflow standard for June in protecting Bay-Delta ecological resources.

Figure 1. Longfin Recruits (Fall Midwater Trawl Index) vs Spawners (Index from two years prior) in Log10 scale. Wet years in blue. Dry years in red. Note the progressive decline in recruits in the last three wet years (06, 11, 17). 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). Source: http://calsport.org/fisheriesblog/?p=1360.

Figure 2. Fall midwater trawl index for longfin smelt versus average June outflow (cfs) 2008-2017. Wet years in blue. Normal years in green. Dry years in red. Source of data: http://www.dfg.ca.gov/delta/data/fmwt/indices.asp?view=single.

Summer Delta Salinity Standards: 2018 Example

Posted on December 29, 2018 by Tom Cannon

In a July 2016 post I recommended a 500 EC (electroconductivity) salinity standard from July-to-mid-August for the western Delta. The longstanding Water Rights Decision 1641 standard includes this only in Wet years. It should apply in all year types unless south Delta exports are at minimum levels.

In summer 2018, a Below Normal, subnormal snowmelt year, Jersey Point salinity was kept near 500 EC through early August (Figure 1) instead of the allowed 740 EC. Was this an adaptive management experiment? If so what benefits were derived from the experiment?

Figure 1. Jersey Point salinity (EC) remained near 500 EC in early summer 2018. The applicable standard was 740 EC 14-day average through August 15.

Benefit #1:
The water temperature in the west Delta in 2018 was kept near 73°F or below (Figure 2), a good thing. In 2016, the previous Below Normal year, EC was allowed above 500 EC (Figure 3) per the existing standard. Water temperature exceeded 73°F to near 75°F (Figure 4), a bad thing, when EC exceeded 500. The reason for the higher early summer 2016 EC and warmer water temperatures was low Delta outflow (Figure 5). Outflow in 2016 was about 7000 cfs, but needed to be near 8000-9000 cfs. In 2018, outflow in late June was 7500-7900 cfs (Figure 6), in part due to relatively low early summer Delta exports (Figure 7) compared with 2016 (Figure 8).

Other Benefits:
It is really too bad that we can no longer look to Delta smelt for response to adaptive management. But I suspect positive response to the 2018 “experiment” occurred in survival of other juvenile Delta fish (e.g., striped bass), shrimp, zooplankton, and phytoplankton. When 2018 data become available, the comparison with 2016 and prior years can be made.

Conclusion:
The salinity standard for the west Delta at Jersey Point and Emmaton should be 500 EC daily average unless south Delta exports are restricted to minimum health and safety levels. The standard should be year-round in all year types. Delta exports should be restricted to the minimum unless the salinity standard is met.