Bay-Delta Fisheries Devastated by Weakened Protections

Water quality standards under the jurisdiction of the State Water Resources Control Board provide bare minimal protections to the State’s major ecosystems in Critically Dry years. But with the extended drought in seven of the past nine years, protections have been weakened to the point where ecosystems and fisheries dependent on them have been devastated. Yes, rice acreage is down 25%1, but fish production is down 95%, with some species lost forever. Salmon numbers have been maintained by hatcheries and trucking hatchery production to the Bay, but not without a huge mortgage on future wild populations. Hatchery salmon already make up over 90% of ocean and river fisheries. Delta Smelt, Longfin Smelt, Steelhead, Green and White sturgeon, Striped Bass, and wild Chinook Salmon populations have declined another 90% in the past four years, after losing 90% in each in the past several decades. Farm production will return, but some fish will not. The ecosystem will return, but with a much different makeup of new food web plankton species from Asia, greater proportions of non-native sport and pan fish, and a greater assortment of the invasive aquatic plants that already fill waterways. The Delta will be featured more often on the Bass Masters Classic.

And what about the Bay? Only a few hundred thousand acre-feet of water of the millions released from reservoirs this summer will reach the Bay. Water quality and marine fish and shellfish will soon show signs of decline. The Bay-Delta is a major nursery for anchovies, herring, and Dungeness crab. Anchovy stocks are already collapsing2. Sea lions are starving and dying.

How hard would it be to at least maintain the antiquated minimum protections adopted in 1995 Bay-Delta Standards? The Bay is “allocated” a base of about 5 million acre-feet of water each year in the form of a base Delta outflow of 7,100 cfs. This standard for critically dry years is the first to suffer from State Board drought orders. The Board has reduced outflows requirements to 3000-4000 cfs (Figure 1). Such low outflows are in reality closer to zero (see earlier blog3). The amount of water “short” from the critical year base in the important February – June period is approximately 300,000 acre-feet. This amounts to less than 5% of the total 10 million acre-feet of reservoir releases into the Central Valley in 2014 and expected in 2015. The amount is less than 10% of the 5 million acre-feet presently in storage in Central Valley reservoirs. The water could be restored to the Bay by reducing water contractor allocations and/or reservoir storage.

The Delta had one plankton bloom that came and went this spring4. Plankton blooms are needed to drive the Bay-Delta food chain. Without freshwater flow to the Bay there will be no blooms and little food through the summer for Bay-Delta fishes. Water quality will suffer as well. The prognosis for the Bay-Delta and other California ecosystems is grim. California fisheries will suffer for decades to come.

Figure 1. Delta outflow as calculated by the California Department of Water Resources for Feb-May, 2015. Top red line represents 7100 cfs minimum standard. Lower red line represents typical weakened level of protection.

Debate on Salmon Trucking Heating Up

A recent FISHBIO blog post1 reported on the CalNev American Fisheries Society annual meeting, where AFS members considered the subject of “off-site” release of hatchery salmon smolts. The general perception is that releases away from hatcheries and the natal river leads to high stray rates, with some estimates of stray rates as high as 90%. The blog post discusses the problems caused by straying to non-natal rivers. The blog post states a concern that the practice of off-site releases will lead to reduced population fitness and genetic diversity, and that reproductive success will be half of wild-origin fish:

“Such losses in biocomplexity are dangerous because of the many threats salmon face in the highly altered Central Valley, and the potential inability of this species to persist if faced with a major environmental disaster, which the current drought in California may foreshadow. Yet despite recommendations from the California Hatchery Scientific Review Group, who warned about increases in straying rates due to off-site releases as early as 2010, managers from across the state have responded to drought conditions by trucking salmon from hatcheries to release sites in the Delta and Bay.”

While FISHBIO’s concerns about straying and genetics are well-founded, it is a little late for the Central Valley Fall Run Chinook. Studies have shown that populations across the Valley are homogeneous, with little or no genetic diversity, and consist mainly of hatchery fish and some natural offspring of hatchery fish. There really are no viable “wild” Fall Run Chinook populations left in the Central Valley. Even runs on rivers with no hatcheries (e.g. Yuba and Cosumnes rivers) are made up almost entirely of hatchery strays.

In making the decision to truck hatchery smolts to the Bay-Delta, Federal and State fisheries managers have recognized the harsh reality that having some salmon is better than having none. No one wants to go back to the bleak escapement years of 2007 to 2009, when less than 100,000 adult salmon per year returned to the Central Valley (compare with 870,000 in 2000 and 200,000-400,000 fish per year since 2009). Recent improvements were in large part due to the smolt trucking program in which 50-80% of Central Valley hatchery smolts were trucked to the Delta or Bay.

Can we have our cake and eat it too? Are there measures we can undertake to improve diversity and reduce straying? Yes, there are many, but they come with costs and with no guarantees.

The hatcheries can be more selective in the genetic material (parents) they use in producing smolts. Hatchery managers can barge smolts to the Bay to reduce straying (during barging, the smolts are suspended from barges in net pens, and thus imprinted on their natal waters during their trip downstream). Hatcheries can mark all hatchery fish to clearly differentiate between wild fish and hatchery fish (generally, hatcheries currently mark only 25% of hatchery juveniles). The Fish and Game Commission could establish mark-selective sport fisheries that allow sport harvest only of hatchery fish. The fisheries agencies could develop Wild Fall Run sanctuaries on some tributaries.

Ultimately, long-standing aspects of Delta operations must change to allow more juvenile salmon to get out of the system and more adult salmon to find their way back to natal streams. Delta exports during the spring are particularly devastating to juvenile outmigrants from the San Joaquin tributaries, including the Mokelumne, because these juveniles are drawn to the south Delta pumps. Low Delta outflow, particularly during spring, magnifies the effects of exports. Opening the Delta Cross Channel during spring may actually improve survival of San Joaquin and Mokelumne juveniles, but only when combined with high Delta outflow. Closure of the Delta Cross Channel gates during the fall, either by design or through fortuitous operational decisions, has reduced straying of Mokelumne River salmon adults to the American River, allowing multiple small pulse flows from the Mokelumne in the fall to help improve adult returns.

Early May Prognosis for Smelt

How are Delta and Longfin smelt doing after my earlier March and April poor prognoses? As predicted, late April – early May surveys indicated extremely low numbers (Figures 1 and 2), far fewer than the record low numbers of 2013-2014 (Figures 3-6).

In the May 4, 2015 Smelt Working Group meeting1, “Members did make a note of the single Delta Smelt larva from April 23, as well as the three Delta Smelt observed during the primary channel CO2 treatment [at Tracy Fish Salvage Facilities], providing that this is evidence of entrainment. These collections occurred despite at or below minimum exports levels, as defined in the Biological Opinion; OMR flows were also at or close to the most positive flows indicated in the Biological Opinion….Salvage of juvenile Longfin Smelt increased to 52 for the week of April 27 through May 3. Some increase was expected as south Delta water warmed. Between April 13 and 15, four juvenile Longfin Smelt were salvaged at the CVP and 12 at the SWP, at the same time, a single larva was observed in the larval fish samples at the CVP and four larvae at the SWP. During the period of April 17 through 23, seven Longfin Smelt larvae were observed at the SWP and one larva at the CVP in larval fish collections. Continued collections in salvage are expected. Overall, catches in the central and south Delta were not sufficient to reach concern levels based on density or distribution… Longfin Smelt larvae and small juveniles will continue to be detected at the salvage facilities until water temperatures surpass 22 deg C.” The fact that any smelt were collected at the two south Delta export facilities should be a grave warning of a larger and very significant “take” of smelt. As stated many times before, the odds of any young smelt reaching the south Delta export facilities without succumbing along the way are infinitesimal. In addition, no smelt will survive in any part of the Delta where water temperature reaches 25°C.

With the prescribed Net Delta Outflow Index at only 4000 cfs and measured outflow nearer to zero, the low salinity zone critical habitat of smelt is in the central Delta. Remaining smelt are being drawn across the Delta from north to south to the export pumps. Under these conditions the first heat wave of late spring will heat the central Delta to lethal 23-25°C levels for smelt. Unless these conditions are changed by increasing outflow and reducing exports, both smelt species may go virtually extinct2 this spring.

Figure 1.  Delta Smelt density distribution in late April 20-mm Survey.  Only three were captured in Sacramento Deep-Water Ship Channel, compared to 20 in previous week’s survey.

Figure 1. Delta Smelt density distribution in late April 20-mm Survey. Only three were captured in Sacramento Deep-Water Ship Channel, compared to 20 in previous week’s survey.

Figure 2.  Longfin Smelt density distribution in late April 20-mm Survey

Figure 2. Longfin Smelt density distribution in late April 20-mm Survey

Figure 3.  Delta Smelt density distribution in late April, 2014 20-mm Survey.

Figure 3. Delta Smelt density distribution in late April, 2014 20-mm Survey.

Figure 4.  Longfin Smelt density distribution in late April, 2014 20-mm Survey

Figure 4. Longfin Smelt density distribution in late April, 2014 20-mm Survey

Figure 5.  Delta Smelt density distribution in late April, 2013 20-mm Survey.

Figure 5. Delta Smelt density distribution in late April, 2013 20-mm Survey.

Figure 6.  Longfin Smelt density distribution in late April, 2013 20-mm Survey.

Figure 6. Longfin Smelt density distribution in late April, 2013 20-mm Survey.

  1. http://www.fws.gov/sfbaydelta/documents/smelt_working_group/swg_notes_5_4_2015.pdf
  2. Virtually extinct means we should not expect to see any next year.

April Delta Bloom Dissipates

The central Delta plankton bloom described in my April 23 post has dissipated (Figures 1 and 2). The bloom was a consequence of long residence time of water in the lower San Joaquin River channel in the central Delta. The increased residence time resulted from a combination of low south Delta exports during April (1500 cfs), low net flows in the lower San Joaquin River (Figure 3), and a prescribed San Joaquin River “pulse flow” (Figure 4). A high “spring” tide period from 4/17-4/25 (Figure 5) likely helped sustain the bloom by restricting Delta outflow (see Figure 3).

The San Joaquin pulse flow had a double benefit: 1) it provided key nutrients to stimulate the bloom, and 2) it reduced south Delta export demand from the bloom area in the central Delta. The pulse flow is indicative of normal San Joaquin April flows, while the extremely low flows subsequent to the April pulse were allowed by the State Water Board in drought-related change orders.

These events are important because they highlight the importance of San Joaquin River inflows and monthly tidal cycles in the Delta for Delta Smelt and Longfin Smelt rearing in the Delta. Smelt are significantly affected by their plankton food supply and the potential entrainment of that food supply into the south Delta export pumps. The pulse flow, like other management actions, should be considered an adaptive management experiment from which valuable insight might be learned for managing the Delta. The bloom was a very rare event, and the circumstances behind it could be important in the future management of the Delta.

Figure 1.  Chlorophyll levels at Blind Point in the western Delta in the San Joaquin River channel during April 2015.  (Source: CDEC)

Figure 1. Chlorophyll levels at Blind Point in the western Delta in the San Joaquin River channel during April 2015. (Source: CDEC)

Figure 2.  Chlorophyll levels in Old River adjacent to Franks Tract in the central Delta during April 2015.  (Source: CDEC)

Figure 2. Chlorophyll levels in Old River adjacent to Franks Tract in the central Delta during April 2015. (Source: CDEC)

Figure 3.  Net flow in the lower San Joaquin River near Jersey Point.  (Source:  USGS).

Figure 3. Net flow in the lower San Joaquin River near Jersey Point. (Source: USGS).

Figure 4.  Net inflow of the San Joaquin River at Stockton in April 2015.  (Source:  USGS)

Figure 4. Net inflow of the San Joaquin River at Stockton in April 2015. (Source: USGS)

Figure 5.  Tidal effect on water surface elevation at Jersey Point in the lower San Joaquin River in April 2015.  A “spring” tide occurred from 4/17-4/25.   (Source:  USGS)

Figure 5. Tidal effect on water surface elevation at Jersey Point in the lower San Joaquin River in April 2015. A “spring” tide occurred from 4/17-4/25. (Source: USGS)

May 2 Spring Tide Affects Delta

The State Board’s weakened standards require a Net Delta Outflow Index of 4000 cfs and limit south Delta exports to 1500 cfs. 4000 NDOI was achieved during the first three days of the month, but a spring tide pushed into the Delta, resulting in actual negative net Delta outflows (NDOs) that were -6000 cfs on May 2. So much salt pushed into the central Delta (see charts below) that South Delta exports had to be reduced from the allowed 1500 cfs to less than 700 cfs. Export reductions were necessary to stop the salt intrusion and to offset the fact that the exported water was becoming too salty. The Smelt Working Group, at its meeting on May 4,1 expressed no apparent concern about the disappearance of the Low Salinity Zone, or about the fact that the population remnants of Delta and Longfin Smelt were pulled into the south Delta.

Meanwhile, the state and federal water project operators dropped Sacramento River Delta inflow from 6900 cfs on April 30 to 5600 cfs on May 2 (oops). They raised Shasta/Keswick releases on May 2 from 7000 to 7500 cfs after lower river flows near Yuba City dropped to 3500 cfs on May 1, as a result of watering up rice fields in the Sacramento Valley. American River (Folsom Reservoir) releases remained settled in at 1000 cfs.

There is simply no excuse for this poor Delta water management. The moon has been around for billions of years and tides are totally predictable. Export water need not have been 600 EC salinity (barely safe for humans and many crops). The several thousand cfs demands for rice fields in the Sacramento Valley could have been restricted for a few days to allow inflow to offset the spring tides in the Delta. Folsom releases could have been bumped up 500 cfs at least for the weekend rafters.

The salt will take a few days to be flushed out by neap tides, but spring tides and salt will soon return. Will Delta water managers be ready?

Salinity (EC) from 4/27-5/7 at Holland Cut in the South Delta on Old River – a primary source of South Delta exports.

Salinity (EC) from 4/27-5/7 at Holland Cut in the South Delta on Old River – a primary source of South Delta exports.

Salinity (EC) from 4/27-5/7 at Threemile Slough -  the connection between the Sacramento and San Joaquin rivers near Rio Vista.  It is a major channel for incoming tides into the central Delta.

Salinity (EC) from 4/27-5/7 at Threemile Slough – the connection between the Sacramento and San Joaquin rivers near Rio Vista. It is a major channel for incoming tides into the central Delta.

Salinity (EC) from 4/27-5/7 at False River - the major connection between the western and central Delta at Franks Tract and Old River.  It is a major channel for incoming tides into the central Delta.

Salinity (EC) from 4/27-5/7 at False River – the major connection between the western and central Delta at Franks Tract and Old River. It is a major channel for incoming tides into the central Delta.