Loss of Salmon in the Sacramento River Floodplain

Posted on September 1, 2015 by Tom Cannon

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:

Blockage of upstream migrating fish behind the Fremont Weir at the head of the Bypass.
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.
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.

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

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.

http://calsport.org/news/wp-content/uploads/2013/07/TC-Colusa-Basin-Drain-Fish-Stranding-1.pdf ↩

Recent Delta Action Further Degrades Low Salinity Zone

Posted on August 10, 2015 by Tom Cannon

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. 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. 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 (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. Note sharp increases after July 19 and August 4 closures of DCC.

It is time to save the Delta Smelt

Posted on July 28, 2015 by Tom Cannon

Causes of the Decline of the Endangered Delta Smelt

There are multiple threats to the Delta Smelt population that contribute to its viability and risk of extinction. Chief among these threats are reductions in freshwater inflow to the estuary; loss of larval, juvenile and adult fish at the state and federal Delta export facilities and in urban, agricultural and industrial water diversions; direct and indirect impacts of the Delta Smelt’s planktonic food supply and habitat; and lethal and sub-lethal effects of warm water and toxic chemicals in Delta open-water habitats.

Temporary urgency change orders by the State Board have allowed reduced Delta outflow and increased Delta salinity. This has moved the Low Salinity Zone further upstream (eastward) into the Delta, thereby increasing the degree of each of these threats. During the past few drought summers, remnants of the population have been confined to a small area of the Low Salinity Zone where water temperatures barely remain below lethal levels. The change orders are an obvious and direct threat to the remnants living in the Low Salinity Zone. Further allowing these weakened standards to be violated is a direct disregard for the remnants of the population. It places them at extraordinary risk by bringing them further into the zone of water diversions, degrading their habitat into the lethal range of water temperature, further degrading their already depleted food supply, and increasing the concentrations of toxic chemicals being relentlessly discharged into the Delta.

Saving the Delta Smelt

The following are measures necessary to save the remnant Delta Smelt population:

Keep the low salinity zone (LSZ) out of the Delta as prescribed in State water quality control plans over the last several decades. This can be readily accomplished by meeting already defined flow and salinity standards and restrictions on Delta exports. The LSZ on the Sacramento channel side should be in the wide open reach of eastern Suisun Bay between Collinsville and the west end of Sherman Island (location of Emmaton standard). It must be kept out of the Emmaton-to-Rio Vista reach just upstream in the west Delta, because this reach is confined and continually degraded by reservoir releases and warm water passing through the North Delta via Three Mile Slough to the interior of the Delta and south Delta water diversions. On the San Joaquin (south) side, the low salinity zone belongs in the wide Antioch–to-Jersey Point reach as prescribed in standards. This can be accomplished in spring and summer of dry years by maintaining prescribed flows, salinity standards at Jersey Point, installation of the False River and Dutch Slough Barriers, and opening the Delta Cross Channel (which results in positive net outflow from the mouth of Old River downstream to Jersey Point in the Central Delta). Maintaining the net positive flows in west Delta channels helps tremendously in getting salmon, steelhead, sturgeon, striped bass, and smelt from upstream freshwater spawning areas to their downstream rearing area target, the estuary’s LSZ. Keeping the LSZ in eastern Suisun Bay, as has always been an objective Delta Water Quality Plans, has huge indirect benefits as well, including greater plankton production, lower non-stressful water temperatures (conducive to growth and survival of all the Delta fish including smelt and salmonids), higher turbidity levels in the LSZ (reduced predation on and improved feeding for Delta smelt), lower invasive Asian clam concentrations in eastern Suisun Bay (which siphon off plankton and larval fish), and lower concentrations of toxins in the LSZ.
Improve the physical habitat of the LSZ. Habitat in eastern Suisun Bay, though far better than that of the west Delta, has been continuously degraded over the past century. Fortunately, there are few levees along the north shore of the Sacramento side. However, the wave-swept shores along Antioch Hills have lost all riparian vegetation except pockets of invasive Arundo. Hillside windfarm and shoreline erosion have filled in shoreline shoals, shallows, bays and alcoves that provided rearing habitat for smelt and salmon (salmon fry are the most abundant fish in these shallows through the winter). Miles of shoreline bays, inlets, and tidal marshes east of Collinsville have been lost. On the south side of the Sacramento channel are the remnants of historic Delta marshes and islands of West Sherman Island and Sherman Lake. Gradually the riparian shoreline and shallow waters are washing away as a consequence of wind as well as ship-wake erosion. Lack of interior marsh channel circulation has also led to grand infestations of invasive non-native submergent, emergent, and floating aquatic vegetation. Like the north shore, the south shoreline of West Suisun Bay on the San Joaquin side is not leveed. Likewise, shoreline and shallow water habitats are degraded, but from industrialization. Large areas east of Antioch to Big Break are degraded much as in the area of Sherman Lake. Both the north and south East Suisun Bay channels are degraded by dredging of the two deep-water ship channels, which has resulted in the loss of shallow shoal, bay, and mudflat habitats. Virtually none of the habitats mentioned above were addressed in the grand BDCP restoration plans for the Bay-Delta. Though some of the areas have been prescribed for restoration in various mitigation plans, virtually no progress has been made toward their restoration in the last several decades.
Stock hatchery raised smelt in the LSZ. The agency-sponsored Delta Smelt conservation hatcheries could be upgraded to production status to provide juveniles to be stocked in the LSZ in late spring and summer. The population is so low now (zero 20-mm and Townet survey indices) that stocking would be helpful if not necessary.
Provide a spring pulse flow into and through the Delta to help smelt fry transport from freshwater spawning areas downstream to the LSZ. This could include passing some Sacramento River flow through the blocked entrance to the Deepwater Ship Channel at the Port of West Sacramento. Delta inflow pulses could be provided by reservoir releases coordinated with infrequent natural flow pulses through the Delta.
Manage tidal flows and Delta hydrodynamics, as well as water quality, on a real time basis to help maintain the LSZ in east Suisun Bay and to stimulate and sustain plankton blooms. Real time management is possible because of the many satellite-accessible data recorders in the Delta, as well as the many frequent biological monitoring surveys being conducted throughout the Bay and Delta. Active adaptive management is possible with the many flow controls available on diversions, reservoir releases, and flow splits (e.g., Delta Cross Channel).

More on Longfin Smelt

Posted on July 20, 2015 by Tom Cannon

Longfin Smelt have declined as other pelagic fish species have over the past two decades. The species was listed in 2009 under the California Endangered Species Act. In a previous blog¹ I described trends in their abundance and distribution in the upper Bay and Delta. Below is a chart depicting the long-term trend in another standard CDFW survey, the San Francisco Bay Midwater Trawl Survey. The index is the average catch for the April and May monthly surveys at a basic array of 28-44 standard stations from San Francisco Bay upstream into the central Delta. Yearling smelt are dominant in the April surveys, while young predominate in the May surveys.

As in other surveys, the index pattern clearly shows a sharp reduction in average catch since 2007. The average catch is particularly low in the last three years. There was no May survey in 2008. Similar patterns were evident in the Fall Midwater Trawl Survey, Summer Townet Survey, Winter Kodiak Trawl Survey, 20-mm Smelt Survey, and the Larval Fish Survey.

http://calsport.org/fisheriesblog/?paged=2 ↩

Longfin Smelt Update – They’re Gone

Posted on July 18, 2015 by Tom Cannon

Back in April, I questioned whether Longfin Smelt, a state-listed endangered fish, are going extinct in the Bay Delta¹. The June surveys are in. The Bay Midwater Trawl, the Bay Otter Trawl, the Townet, and the 20-mm Survey show Longfin are at record lows with only a few caught in the Bay². One only has to compare 20-mm Survey results for June over the past three years to see the trend. Going, going, gone.