Delta June 2019

Water year 2019 has been a very wet year.  Yet salmon and sturgeon survival was compromised by low flows and high water temperatures in the Sacramento River this spring.1 Young salmon survival has been further compromised by low flows, high exports, and high water temperatures in the Delta this past June.

Many of the wild smolts produced in Central Valley rivers this year entered the Delta in May and left (or died) by the end of June, as observed in Delta export salvage collections (Figure 1).  Many of the wild smolts captured in the south Delta likely originated from San Joaquin tributaries.  South Delta exports were near maximum at 10,000 cfs, about 70-80% of San Joaquin inflow to the Delta and 20% of total Delta inflow.  The high exports caused lower flows and associated high water temperatures (>20oC) in the Delta channel of the lower San Joaquin River (Figure 2), and contributed to similarly high temperatures in the lower Sacramento River channel (Figure 3).

The high Delta water temperatures (>20oC) compromised the survival of the salmon smolts in June.  Reducing the export limit to 5000-6000 cfs in June of this wet year would have kept the water temperature near a 20oC limit.  The water quality standards in the 1980’s and 1990’s under D-1485 had a 6,000 cfs June export limit.  In the past two decades under D-1641, the June export limit changed to 65% of total inflow.

New Delta water quality standards should provide export limits and inflow/outflow minimums that protect salmon through the spring months.

Figure 1. Chinook salmon salvage at south Delta export facilities in 2019. Note the prevalence of wild (non-hatchery) smolts in May-June.

Figure 2. Water temperature and tidally-filtered flow at Jersey Point in the lower San Joaquin River channel of the Delta in June 2019.

Figure 3. Water temperature and tidally-filtered flow at Rio Vista in the lower Sacramento River channel of the Delta in June 2019.

 

 

Sacramento River Salmon Opener Compromised

The California Department of Fish and Wildlife announced in May that the salmon season on the Sacramento River would commence below Red Bluff on July 16, with high expectations and expanded limits.

 “California’s inland salmon anglers can look forward to a better salmon fishing season than last year. A projected return of 379,600 spawning Sacramento River fall-run Chinook Salmon to Central Valley rivers has allowed fishery managers to return to a two salmon daily limit with four salmon in possession. This is a welcome increase over last year’s regulations, which restricted anglers to one salmon per day and two in possession.”

Yet despite near record water and a full Shasta Reservoir, the federal government is compromising the run with high water temperatures from low reservoir releases and high river diversions that violate state water quality regulations and water right permit requirements.

River flow near Red Bluff is just above 12,000 cfs (Figure 1), about 1000 cfs below average for this time of year.  River flow in the river a hundred miles downstream, upstream of the mouth of the Feather River, is just below 7000 cfs, also slightly below average (Figure 2).  The flow difference between the two locations reflects water deliveries to federal water contractors near 5000 cfs.

The high diversions and low flows result in high water temperatures in the lower river (Figure 3) that will compromise the fishery opener as well as survival and egg production of this fall’s spawning run.  The salmon run is already in a long-term decline (Figure 4) from poor water management and violations of standards and permits conditions.

Why allow the federal government to squeeze out more of California’s precious water and salmon?  Increasing Shasta releases or reducing diversions, or a combination thereof, by about 1000-2000 cfs should protect the migrating salmon and provide a better fishery opener.  With triple-digit weather forecasted for the latter half of July, it is imperative that river flows be increased.

Figure 1. Sacramento River flow near Red Bluff June-July 2019.

Figure 2. Sacramento River flow near Grimes at Wilkins Slough June-July 2019.

Figure 3. Sacramento River water temperature below Wilkins Slough June-July 2019. Note that water quality standard is 68oF, above which salmon become stressed.

Figure 4. Sacramento River fall-run salmon escapement 1952-2018.

Why is Water Temperature in the Delta so important? Why there should be a water quality objective in the Delta for water temperature.

The rivers flowing into the Delta are generally cool.  The Bay is generally cool.  But the Delta gets warm (>20oC, 68oF) from late spring into early fall.  Rivers have a water quality standard limit of 68oF.1 The Delta should too.

Salmon, smelt, and steelhead are cool water fish that use the Delta for major portions of their life cycle.  Water temperatures above 68oF are stressful, leading to poorer growth, higher predation, lower survival, and early exits from Delta critical habitats.  One reason for the stress is that warmer water holds less dissolved oxygen.  When water temperature exceeds 68oF, dissolved oxygen falls below 8 parts per thousand (ppt), which is stressful to fish.  In eutrophic (high organic loads with lots of aquatic plants) waters like the Delta, dissolved oxygen can get even lower, near the minimum state standards (6-7ppt), especially at night.

Delta waters are cooler in wet years because of higher flows and generally cooler spring air temperatures.  There is no doubt that low river inflows, higher exports, and low Delta outflows can exacerbate high Delta water temperatures, especially during hot periods of summer.  There is also plenty of evidence that higher inflows, lower exports, and higher outflows during exceptionally warm weather can help minimize high water temperatures.

Delta waters are cooler when inflows are higher and cooler.  The lower reaches of rivers that enter the Delta are cooler with higher flows.  Maintaining high river inflows with the associated cooler water helps maintain Delta water temperatures.  It takes approximately 20,000 cfs of Sacramento River inflow at Freeport to the Delta to maintain inflow water temperature near 68oF in summer (Figures 1-3).

The central Delta flow inputs are also cooler in late spring under higher Delta inflows, as exemplified by water temperature and flow comparisons between dry 2015 and wet 2011, 2017, and 2019 (Figures 4 and 5).  This comparison dispels the argument that that water temperature in the Delta is wholly dependent on air temperature and is not affected by flow.

There is evidence that increasing diversions and decreasing flows in warmer weather (Figures 1 and 3) increases water temperatures.  This is another reason to increase Delta river inflows during warm weather.  A Delta water temperature standard/objective would potentially require episodic higher Delta inflows to offset higher warm weather diversions, in addition to a sustained inflow near 20,000 cfs in summer.

Figure 1. Water temperature and Sacramento River flow in summer 2016.

Figure 2. Water temperature and Sacramento River flow in summer 2017.

Figure 3. Water temperature and Sacramento River flow in summer 2018.

Figure 4. Water temperature in late spring in Georgiana Slough 2011, 2015, 2017, 2019.

Figure 5. Daily average flow in late spring in Sacramento River at Freeport 2011, 2015, 2017, 2019

Improved Yolo Bypass Fish Passage

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.

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

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 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 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 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 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 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 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.

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

 

Shasta River Update – April 2019

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 (>65oF) 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.