Author Archives: Tom Cannon

It is time to save the Delta Smelt

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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:

  1. 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.
  2.  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.
  3. 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.
  4. 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.
  5. 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

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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.

Longfin Smelt Average Catch Apr-May Baay Mid-water Trawl 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.

Longfin Smelt Update – They’re Gone

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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.

Longfin Smelt Survey 2013

Longfin Smelt Survey 2014

Longfin Smelt Survey 2015

Corps gears up for summer fish operations – June news release

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Sorry to say this is not in California – it’s the Columbia River system with its eight major mainstem dams.1  Summer “spills” have been the heart of the Columbia salmon recovery because they have helped smolts reach the ocean. The cost of “spills” is primarily lost hydropower to federal and state utilities. That was the price for keeping all the dams.

In the Central Valley the dams were built for hydropower, flood control, and water supply. Here we have Settlement Contractors with water rights that preceded the dams, who agreed to contracts that allowed the dams to be built. These folks come first in line when it comes to federal and state water rights to stored water. After these folks come the big water districts and urban water contractors of the Central Valley Project and the State Water Project.

The Columbia dams also have fish ladders that allow adult salmon to reach tributaries and headwaters and require smolts to pass the dams to reach the ocean. In the Central Valley we have wild and hatchery salmon populations below the large dams, and there are no fish ladders. (Note there are also no ladders on the big Grand Coulee and Hells Canyon Columbia system dams.)

The equivalent action of “summer spills” on the Columbia would be “spring spills” from Central Valley reservoirs. However, with stored water over-appropriated (even in most flood years when too little storage is carried over for the following year), there really is no water for “spring spills” without taking water away from people, mostly irrigators, who expect to get that water. (Note there are some higher flow requirements on the Sacramento and San Joaquin rivers and from the Delta in wetter years, but these are not near the amount of water in “spills”.)

Would Central Valley salmon benefit from “spring spills”? Yes, substantially, especially in non-flood wet and normal years. Obviously, there would be insufficient water for “spills” in some drier years and even in some normal years.

What do they do on the Columbia River in dry years? They have a smolt collection and transport program that collects wild and hatchery smolts and transports them with trucks and barges around the dams and to the estuary.

The federal recovery plan for Central Valley salmon does not include either spills or transport, but instead requires trap-and-haul above the dams. This is important and likely essential to prevent extinction of some salmon races (e.g., winter and spring run), but we also need spill and transport programs downstream of the dams. If we want to retain these fisheries, we must invest in spill and transport programs now. These programs, like those on the Columbia, should be paid for by those benefitting from the flood control, electricity, water supply and recreation provided by the dams.

Splittail – Native Delta Minnow

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Splittail – Native Delta Minnow

Splitail Indices Graph

Splittail, formerly listed as threatened under the federal Endangered Species Act (1994), were delisted in 2003 after nearly a decade of wet years that brought about apparent recovery.1 Dr. Moyle’s recent warnings about other Delta native fish2 after nearly a decade of drought surely apply to splittail. Once the most abundant fish in late spring and early summer salvage collections at the south Delta export facilities, splittail are now rarely collected3. Once common in dry periods (1987-1992) and prone to abundance in wet periods (1993-2001), they are now rare in dry periods (2007-2009, 2012-2015). Because they live 5-8 years, they are able to spawn successfully in infrequent flood years, 2011 being a good example. The modest production from 2011 will be five years of age in 2016. One can only hope that 2016 will be a wet year.

I argued at a January 2001 CALFED workshop on splittail4 for retaining the listing of the species as threatened; however the consensus was “statistical power to detect real population trends in the past 30 years is low, thereby undermining confidence in any estimates of extinction risk based on abundance”. The 15 production years since the workshop have clearly added to the “statistical power”. I would argue for relisting splittail, if only for the reason they are now far less abundant then they were prior to the original listing, and to ensure something is done to protect them over the next several years so they indeed do not go extinct.