Category Archives: Bay-Delta

Part 3 – Trinity River Salmon

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This is part 3 of a four-part series on the effects of the Shasta-Trinity Division on Sacramento and Trinity-Klamath salmon. Part 1 is an introduction to the series. Part 2 is a discussion of the effects of the Shasta-Trinity Division on Sacramento River salmon. Part 3 is a discussion of the effects of the Shasta-Trinity Division operation on Trinity-Klamath salmon.

Operations of the Shasta-Trinity Division affects Trinity River salmon as well as salmon in the lower Klamath River downstream of the mouth of the Trinity River. The main effect on the Trinity-Klamath salmon comes from the export of approximately half of Trinity Reservoir’s inflow to the Sacramento River, resulting in lower Trinity storage. This in turn may cause lower Trinity-Klamath flows and higher water temperatures in the Trinity River and lower Klamath.

National Marine Fisheries Service (NMFS) is in the process of conducting a separate consultation on the effects of the Shasta-Trinity Division operations on listed Coho salmon in the Trinity River. NMFS is committed to ensuring appropriate coordination between the analysis and results of Sacramento Winter Run Opinion and the forthcoming Coho opinion. The NMFS OCAP BO RPA1 will be analyzed in the Trinity Coho Opinion, and the OCAP BO may be adjusted as necessary to avoid jeopardy to Trinity-Klamath Coho salmon and adverse modification of their critical habitat.

The biggest threat to Trinity salmon results from the drawdown of Trinity Reservoir as Trinity water is exported to the Sacramento River. Without adequate carryover storage, Trinity reservoir cannot be counted on to provide sufficient cold-water flow to the Trinity and lower Klamath Rivers. Without a sufficient cold water pool in Trinity Reservoir, warm water from the reservoir can threaten the Trinity, Lower Klamath, and Sacramento River salmon. While the large die-off of salmon in the lower Klamath in 2002 may not be directly attributable to low warm water flows to the upper Trinity River below Lewiston Reservoir, pulses of cold water from Trinity Reservoir in late summer under conditions like 2002 have averted similar die-offs in 2014 and 2015. Pulses of cool water released from Trinity Reservoir continue this month despite unsuccessful attempts by Central Valley water contractors to stop that action. So far, the cold water pool in Trinity Reservoir appears adequate to save Trinity and Klamath River this year despite its ongoing depletion by exports to the Sacramento River. Approximately three quarters of the water released from Trinity Reservoir this summer has gone to the Sacramento River.

Trinity Reservoir storage in acre-feet over the past three years.

Trinity Reservoir storage in acre-feet over the past three years.

Trinity Reservoir water export to Sacramento River via Whiskeytown Reservoir summer 2015.

Trinity Reservoir water export to Sacramento River via Whiskeytown Reservoir summer 2015.

Trinity Reservoir water released to Trinity River from Lewiston Reservoir summer 2015. Note recent flow releases to flush and cool the lower Trinity and Klamath.

Trinity Reservoir water released to Trinity River from Lewiston Reservoir summer 2015. Note recent flow releases to flush and cool the lower Trinity and Klamath.

Temperature of water released from Lewiston Reservoir in spring-summer 2015.

Temperature of water released from Lewiston Reservoir in spring-summer 2014.

Temperature of water released from Lewiston Reservoir in spring-summer 2015.

Temperature of water released from Lewiston Reservoir in spring-summer 2015.

  1.  The Reasonable and Prudent Alternative(s) in the National Marine Fisheries Service’s Biological Opinion for the long term Operations and Criteria Plan for the State Water Project and the Central Valley Project. ↩

Summer 2015 – Delta Smelt Update

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Delta Smelt are virtually extinct from the Bay-Delta. Few have survived the extreme conditions of Delta operations during this fourth summer of drought.

Early June Surveys

The catch of Delta smelt in the early June 20-mm survey for Delta Smelt was fourteen, twelve in the Sacramento Deep Water Shipping Channel (Figure 1). This compares to the record low of 22 last year.

Figure 1. The distribution of Delta smelt catch in early June 2015 20-mm Survey. (Source: CDFW)

Figure 1. The distribution of Delta smelt catch in early June 2015 20-mm Survey. (Source: CDFW)

The plots for the early June survey for the past four drought years are shown in Figures 2-5. Obviously the numbers are down even from last year. The main difference is that only one was captured in the low salinity zone (in Sacramento River channel on north side of Sherman Island). This zone of brackish water, generally with cooler water and high productivity, is again in poor condition due to lack of freshwater inflow from weakened water quality standards during the present drought. The effect of weakened standards in 2014 and 2015 (4000 cfs Delta outflow instead of 7000 cfs) is quite evident by comparing these last two years with the previous three drought years when standards were not weakened.

Figures 2-5. Distributions of Delta smelt in early June 20-mm surveys in 2009 and 2012-14. (Source CDFW)

Figures 2-5. Distributions of Delta smelt in early June 20-mm surveys in 2009 and 2012-14. (Source CDFW)

Late June and Early July Surveys

The July standard of 4000 cfs Delta outflow was also weakened to 3000 cfs. The lower outflows lead to a smaller, warmer low salinity zone (further upstream in the hotter Central Valley away from the Bay “breeze”). In addition, under lower flows, more of the low salinity zone is drawn into the central Delta by Delta exports. Surveys #8 (late June) and #9 (early July) each captured only one Delta smelt, as compared to 20 and 2 in the respective surveys in record low 2014.

Initial results of the Summer Townet Survey (CDFW unpublished data) for June indicated record low numbers of Delta smelt (near zero).

July and August Surveys

The final 20-mm Survey in July and the July and August Townet Surveys only caught one Delta Smelt each. Both fish were caught in the Sacramento Deep Water Ship Channel (same site as large green dot in Figure 1). None were captured this summer in their normal nursery grounds in the Low Salinity Zone in any surveys. The poor prognosis for Delta smelt has been downgraded to miserable. For previous recommendations on improving conditions for Delta smelt see a previous post1.

FISHBIO takes on Stripers – again

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In a recent blog post1, FISHBIO again discuss the role they allege that Striped Bass are playing in limiting salmon production in the Central Valley. They bring up the 5-year-old proposal to reduce regulations on the Striped Bass fishery that was soundly rejected by fishermen, resource managers, environmentalists, and scientists alike. They state that despite the fact that anglers spend more than ten times the hours spent fishing for stripers than for salmon, the economic benefit of striper fishing is far below that of salmon fishing.

Well, assuming the raw economic numbers are true:

  1. The State closed the Striped Bass commercial fishery a century ago.
  2. The Striped Bass fishery is year-round and throughout most of the Central Valley, whereas the salmon fishery is seasonal and more localized. There must be some social value in diversity.
  3. The economic status of Striped Bass fishermen is far more diverse than salmon fishermen. There must be some social value in supporting a broader range of citizens.
  4. Many California residents are from the East, where stripers are king and there are no salmon.
  5. Much of the salmon fishery value derives from the ocean fisheries, whereas the striper fishery is focused on Bay-Delta and inland waters. The relative cost of fishing in these regions is very different.
  6. Most of the salmon fishery value (over 90%) is derived from hatchery fish. The Striped Bass supplemental rearing program was closed over a decade ago. The striper effort was ten times higher then, the number of stripers was up to ten times higher in the past, and the economic value was also likely ten times higher.

The other portion of FISBIO’s argument concerns the role of Striped Bass predation in salmon declines.

  • “ During the early 1900s, striped bass thrived alongside salmon, but as salmon declined over the latter part of the century, the impact of these introduced predators took a proportionally greater toll on the salmon population.” There is no evidence to support this statement. Stripers have declined more than salmon. There are still 30-million hatchery smolts for a much smaller striper population to feed on.
  • “Controlling predators to help their prey species is not a new idea; other states have been controlling non-native and native predators with measured success for decades.” No doubt the greatest “predator control” success (over 90%) has been on the Striped Bass population by the federal and state export pumps over the past two decades.
  • “While California has failed to act, some political support for predator control has recently developed at the federal level. Multiple bills currently proposed in Congress include provisions for advancing predator control in the Delta.” These bills were sponsored by San Joaquin Valley congressmen and have little chance of passing.
  • “While these federal actions alone may not be sufficient to produce population increases in some threatened or endangered species, there is evidence that predation is a major barrier to salmon recovery, and the proposed legislation demonstrates a changing mindset toward controlling predation of declining species.” There is no evidence that predation by Striped Bass on wild threatened salmon runs is even in the top ten reasons for their declines. The “mindset change” is to divert attention away from the real reasons for threatened salmon declines, or from having to pay for their recovery.

Finally FISHBIO speaks to “changing mindsets” of anglers: “Perhaps the biggest hurdle to controlling non-native species like striped bass will be changing the mindset of the fishing community that cares deeply about these popular predators.” They mean that anglers should accept the false premise that Striped Bass are the problem and should allow them to be exterminated.

Loss of Salmon in the Sacramento River Floodplain

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The loss of juvenile and adult salmon in the Sacramento River floodplain has been a problem for many decades. The problem is largely the result of the construction of dams, agricultural drains, and flood control systems. The problem is acute, and although well documented and quite obvious, little has been done to resolve it. The fixes are not cheap and no one wants to get stuck paying for them. In addition, potential fixes have been hoarded as potential mitigations for large public works projects like the Bay Delta Conservation Plan and its associated Delta Tunnels.

The Problem

Figure 1 is a map of the Sacramento Valley with arrows showing some of the major locations of the problem. Much of the problem is the result of limitation or blockage of fish passage; another major factor is stranding. Adult salmon, sturgeon, and steelhead migrating up the Sacramento River become attracted to the high volumes of Sacramento water exiting the Sutter and Yolo Bypasses (adult fish movement is shown by red arrows in Figure 1), only to be blocked at the high weirs at the upstream end of the bypasses (Figures 2 and 3). Even modest bypass flows in drought years can cause attraction and subsequent mortality (Figure 4).

Young salmon emigrating downstream from upriver spawning grounds pass into the bypasses (green arrows in Figure 1) and adjacent basins in huge numbers. Many become stranded and lost when flows and water levels decline when weirs quit spilling (the river can drop ten feet overnight and quickly cease spilling into bypasses).

Landowners Seek Solution

In one of the areas, the Yolo Bypass, local landowners and stakeholders are seeking a solution. They are addressing three critical issues:

  1. Blockage of upstream migrating fish behind the Fremont Weir at the head of the Bypass.
  2. Blocked fish migrating to their deaths into the Colusa Basin from the Bypass via the Knights Landing Ridge Cut1. Adult migrants are also attracted directly to Colusa Basin Drain outlet even when Fremont Weir does not spill.
  3. Increasing survival of young salmon spilled into the Yolo Bypass by augmenting flows and improving habitats and habitat connectivity.

The first issue often occurs each time the weir spills at flood stage (generally one in three years, although it has not spilled significantly since 2006 because of drought). The bandaid treatment is shown in Figure 2. Stakeholders have advocated a short-term solution for passing fish via a “small notch” in the Fremont Weir to pass fish over the weir into the river; however, long-term agency plans call for a more contentious “large notch” in the weir.

The second issue requires the opposite solution, placing a fish-blocking weir at the outlet of the Knights Landing Ridge Cut to stop adult salmon, sturgeon, and steelhead from migrating upstream into the Colusa Basin. Landowners are working with the California Department of Water Resources and Reclamation toward building such a weir. For now the bandaid is a fish trap and fish rescues such as that shown in Figure 2.

The third issue can be resolved by engineering the bypass floodplain to provide better habitat and connectivity for the salmon including high and longer-sustained flows from the Fremont Weir (via a “notch”). Local landowners have developed an array of actions to provide habitat and connectivity.

In my experience, placing leadership and responsibility for developing and implementing actions in the hands of local stakeholders has worked best to help save fish. “Locals” can be surprisingly adept at coming up with viable solutions to fisheries problems.

Map of Sacramento Valley showing levees and flood control system weirs and bypasses

Figure 1. Map of Sacramento Valley showing levees and flood control system weirs and bypasses. Gray area agricultural basins are generally below the elevation of the river and bypasses. The flood control system was initially designed to convey flood water and historic foothill mining debris through the Valley. Adult salmon (as well as sturgeon and steelhead) are attracted to the high flows entering, passing through, and exiting the Sutter and Yolo Bypasses (such adult migration is shown with red arrows). Many cannot successfully complete their passage either becoming lost or blocked at the upstream end by weirs (located at the blunt end of the green arrows). Many young salmon become stranded in the basins and bypasses after entering in spill over weirs during floods. (Map source: http://baydeltaconservationplan.com/Libraries/Dynamic_Document_Library/Fact_Sheet_-_Sac_River_System_Weirs_and_Relief_Structures.sflb.ashx )

Figure 2. Sturgeon being rescued below a Sacramento River bypass weir

Figure 2. Sturgeon being rescued below a Sacramento River bypass weir

Moulton Weir 1997

High storm flows in late December 2014 into the Yolo Bypass from the Knights Landing Ridge Cut attracted many salmon to the northern end of the Bypass

Figure 4. High storm flows in late December 2014 into the Yolo Bypass from the Knights Landing Ridge Cut attracted many salmon to the northern end of the Bypass. When storm flows receded after several days, hundreds of adult salmon became stranded in winter-fallow fields that had been flooded. Many more salmon likely passed successfully into the Colusa Basin drain system only to find no route to spawning grounds in the upper Valley.

Recent Delta Action Further Degrades Low Salinity Zone

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Recently, Reclamation closed the Delta Cross Channel (DCC) (Figure 1) near Walnut Grove to reduce salinity at the State Board’s compliance point at Threemile Slough. Normally, the DCC is open in summer to allow fresh water into the central, east, and southern Delta to maintain low salinity water for exports and for agricultural and municipal diversions. However, low fresh water inflows to the Delta due to the drought have resulted in salinity levels exceeding the required 2.78 EC level at Threemile Slough. Closing the DCC effectively forced more of the fresh -+water inflow from the Sacramento River toward the western Delta and Threemile Slough, reducing EC at Threemile Slough significantly (Figure 2).

Figure 1. Flow through the Delta Cross Channel in July and August 2015

Figure 1. Flow through the Delta Cross Channel in July and August 2015. Zero flow indicates the gates are closed. Gates are normally open in summer.

Figure 2. Salinity (EC) at Threemile Slough compliance point in western Delta

Figure 2. Salinity (EC) at Threemile Slough compliance point in western Delta. Salinity (EC) must be maintained below 2780 EC on a seven day average. Salinity exceeded the target on July 18. Closing the DCC on July 19 immediately reduced salinity to the compliance level. Subsequent closing of the DCC on July 25 brought salinity back up to and exceeding pre-closure levels. As the seven day compliance target was again exceeded August 1-3, the DCC was again closed on August 4 to again bring the salinity into compliance.

This rollercoaster salinity management in the Delta causes serious degradation to the Low Salinity Zone in the western Delta in the form of higher water temperatures. The higher water temperatures occur when warm northern Delta waters are moved west with the higher flows. These higher temperatures are evident at all the western Delta gages maintained by the Department of Water Resources and the US Geological Survey. The water temperatures change is approximately 2°F, which is significant and detrimental to the remnants of the Delta Smelt population trying to survive this extreme summer drought. Water temperatures have increased from 73° to 75°F, essentially creating lethal conditions for the remnant smelt.

The influx of warm water is apparent at Rio Vista where the Sacramento River enters the western Delta (Figure 4). Not only did the water temperature immediately rise with the higher flows on July 19, but the higher temperatures were sustained after the flows receded on July 25.

Overall, the unprecedented closure of the DCC in summer leads to rapid and significant changes in flow, salinity, and water temperature in the Delta that are likely detrimental to Delta native fishes including the Delta Smelt.

Figure 3. The map annotations depict changes from recent closures of the DCC

Figure 3. The map annotations depict changes from recent closures of the DCC (located at blue X). The closure reduced flow in the Mokelumne channels (dotted red line) by 3000 cfs. Georgiana Slough (west side of Tyler Island) flow increased 1000 cfs. Flow into the Sacramento channel at Rio Vista increased 2000 cfs. Net water temperature increase throughout the western Delta was about 2°F.

Figure 4. Water temperature at Rio Vista Bridge in July-August 2015

Figure 4. Water temperature at Rio Vista Bridge in July-August 2015. Note sharp increases after July 19 and August 4 closures of DCC.