Low Flows – Deadly Water Temperatures

Posted on August 22, 2016 by Tom Cannon

Low flows in the Sacramento River and Delta lead to deadly water temperatures for Central Valley salmon, steelhead, sturgeon, and smelt, including six state or federally listed endangered species. Water quality standards and operating requirements for the state and federal water projects should include new flow limits to protect fish.

Sacramento River

Salmon, steelhead, and sturgeon are subjected to deadly spring and summer water temperatures when lower Sacramento River flows fall below 5000 cfs as measured at Wilkins Slough (Figure 1). Low flows and high water temperatures lead to poor survival and increased predation, and block migrations of adult salmon.

Delta

Low flows through the lower Sacramento River channel in the Delta also lead to deadly water temperatures for salmon and smelt. When Delta inflow falls below 10,000 cfs, water temperatures become deadly for Delta Smelt (Figure 2) and salmon (Figure 3).

Figure 1. Daily average water temperature and river flow in the Sacramento River at Wilkins Slough (RM 125) 2007-2016. Water temperatures greater than 75°F are lethal to salmon and sturgeon, and block salmon migration. The water quality standard for the lower Sacramento River is a limit of 68°F. Temperatures above 68°F are stressful to salmon, sturgeon, and steelhead, and lead to increased risk of predation, lower survival, and poor reproductive success.

Figure 2. Daily average water temperature and river flow in lower Sacramento River near Freeport. Water temperatures greater than 73°F are lethal to smelt and block salmon migrations.

Figure 3. Daily average water temperature in the south Delta at Clifton Court 2009-2016. Water temperatures greater than 25°C (77°F) are lethal to salmon and smelt.

Smelt Extinction and Recovery: The Path Forward

Posted on August 11, 2016 by Tom Cannon

The March 29, 2016 Delta smelt symposium, part 4 (“Panel Discussion of the Path Forward”) offered some hope but few specific strategies for Bay-Delta smelt recovery. My own presentation and other presentations earlier in Part 2, focused on how smelt got to the brink of extinction. In Part 4, the panel of experts was asked to offer ways to bring smelt back from the brink. Reading the transcript and watching the video of the discussion, there did not appear to be any specific array of actions or coherent strategy offered by the panel. But on further review, I did find some nuggets that when put together sketch a reasonable course of action.

First, though, it is important to point out that over the past two decades there were two episodes that stopped extinction and brought some (albeit modest and short-lived) recovery with the help of Mother Nature. The D-1641 water quality standards and the actions required by the Delta Smelt Biological Opinion actions did help. The symposium should have focused more on those actions that helped, in order to see what further is needed. Admittedly, the fact that recovery episodes were not more frequent makes this difficult. It also does not speak well for 20 years of Bay-Delta adaptive management, which in large measure was a test to see how far the Bay-Delta ecosystem could be stressed by taking more and more water without breaking it. Now that the ecosystem is broken, it is harder to see what helps and what does not.

Here is what I assembled from the panel’s discussion as a reasonable strategy to put the smelt and the Bay-Delta ecosystem back on a recovery course again.

Yolo Bypass – Cache Slough Complex

Simply putting more Sacramento River water down the Bypass might improve the Complex and transfer more of its nutrients, turbidity, and plankton (and smelt) to the north Delta and eastern Bay low salinity zone. Available water sources include the Colusa Basin Drain and Fremont Weir. The large Sacramento River agricultural diversions that feed the Drain are minimally used outside the April-October irrigation season. Present mandates and plans to notch the Fremont Weir would provide a direct source of Sacramento River water to the Bypass. A long-mandated relocation of the North Bay Aqueduct intake from the Cache Slough Complex to the Sacramento River would also help.

Sacramento Deep Water Ship Channel

Mentioned several times as the last refuge of Delta smelt, the Ship Channel from the Port in West Sacramento to the lower end of Cache Slough offers potential in improving conditions for smelt. The closed gate at the upper end of the Ship Channel could be opened at key times to pass Sacramento River water into the upper channel to help flush smelt and nutrients into the north Delta, or simply to enhance smelt survival in the channel itself and in the lower Cache Slough Complex. A panelist suggested dredging the channel. Opening it in summer would cool the channel and possibly the lower Complex because the opening is near the mouth of the American River with its cool outflow.

Nutrients

The Panel suggested Increasing nutrients, specifically nitrogen, as a means of boosting plankton productivity and smelt survival in the Delta. Ironically, the Sac Regional Treatment Plant is being forced to reduce its ammonia and nitrogen inputs to the Delta. But the suggestion holds much promise because plankton blooms and turbidity from them are necessary staples of smelt critical habitat. A recent spring plankton bloom coincident with a San Joaquin River flow pulse and low Delta exports suggests one option for increasing nutrients and plankton blooms. Another option is the above-mentioned flow through the Bypass and Ship Channel. Not exporting higher nutrient low salinity zone water is another. Employing the Head of Old River Barrier would force more of the high nutrient San Joaquin water into the Central Delta and away from the south Delta export pumps.

More Delta Outflow to the Bay

Almost everyone on the panel suggested the need for more flow to the Bay to help the smelt. The smelt are simply far better off in wet years. But no one on the panel suggested upgrading the Delta Outflow requirements in the Bay-Delta D-1641 water quality standards, a process that has been ongoing for nearly a decade. Relaxation of the outflow requirements in the past four years of drought proved disastrous for smelt, the kind of adaptive management experiment we could do without. More outflow moves smelt into better habitat in Suisun Bay and Marsh. It also keeps them away from the export pumps, Delta agricultural diversions, and the warmer lower-turbidity confines of the Delta channels with their profusion of warm water competitors and predators. A panel member noted the difficulty of “finding” more water for outflow. The water is there; the need to is export less of it.

Exports

Several panelists suggested there has been too much emphasis on Delta exports, and that we should be focusing more on other solutions like improving habitats. While physical habitat improvements could help, the fact is that Delta pelagic habitat so essential to smelt and other Delta fishes has been severely degraded by exports (and lower outflows) at an ever increasing rate over the past four decades. Global warming is further adding to the stress. None of the panelists mentioned the benefits of export restrictions in the D-1641 standards or biological opinions. The agricultural community screams to weaken these restrictions, in part from the lack of recognition of their benefits.

Hatchery

Several panelists expressed the opinion that the species is protected from extinction by holding them in captivity in two conservation hatcheries. While that may be noble, it is not going to save the Delta or smelt. The option of expansion to production hatcheries was barely discussed, because of an underlying concern of where to put the hatchery fish given the poor existing habitat. But one panelist suggested stocking may be necessary to provide enough natural spawners to allow them to find one another during the spring spawn. Regardless, there are times and places where better habitat occurs such that if more smelt were added, it would benefit the population (e.g., when X2 is downstream of the Delta in the fall).

Predators

The panel mentioned predators, but only as one of the negative changes that have occurred over the past several decades. The panel discussed habitat enhancements as a means of reducing predators or their access to smelt. There was mention of increasing nutrients to increase phytoplankton food and turbidity, to shade out aquatic plants that shield non-native predator fishes. This holds promise if export operations do not replace good spatial habitat with incoming warm low turbidity river and reservoir water. The panel thankfully did not speak of directly removing Delta predators as a solution to the problem, a suggestion fostered by the ag community.

The Solution Package

As a group, the strategies mentioned above offer a reasonable short-term solution package to save the Delta smelt. Nearly all the actions can be immediately implemented, or at least started. As a followup to the symposium, I suggest a workshop to develop a plan for such a solution package to guide recovery during the coming years of water battles over the WaterFix (Delta Tunnels), the update of the Bay-Delta Water Quality Control Plan, and the revision of the biological opinions for the long-term operation of the CVP and SWP.

Splittail Update

Posted on August 3, 2016 by Tom Cannon

Since I last posted about splittail, there has been little sign of their recovery in the Bay-Delta. Flooding in the Sacramento Valley brought modest production in 2016, but a dry year in the San Joaquin Valley brought little there. Numbers observed in summer south Delta pumping plant salvage are now very low (chart), with little evidence of recovery of the population. The 2011 year class of 5 year olds, the last good wet-year year class, produced minimal offspring in the past three years. It is fair to say that the recovery potential for the species is improbable. The next several years will be the last for the 2011 year class, leaving the viability of the species in question. As I stated in the earlier post, splittail should not have been removed from the federal list of endangered species.

Salvage of Splittail at south Delta export facilities from April 2011 to July 2016.

Delta Update – August 1, 2016

Posted on August 1, 2016 by Tom Cannon

Just a quick update on Delta fisheries on August 1, 2016. Delta outflow this spring-summer for this below-normal water year was as expected, except for the pulse of up to 14,000 cfs in the July experiment to help Delta Smelt (Figure 1). Year 2000, an above-normal year and a pre-Pelagic Organism Decline year, is shown for comparison.

Figure 1. Delta outflow May-July 2000 and 2016.

Striped Bass

My earlier optimism for this year’s striped bass production continues to fade. I continue to believe that the poor success is related to poor early summer Delta outflow based on comparison with year 2000, the last decent year class produced by striped bass in the Bay-Delta as determined by the June Summer Townet Survey. Figures 2 and 3 show abundance and distribution in 2000 and 2016, respectively. Densities were an order of magnitude higher in 2000, after spring larvae abundances were similar between the two years. Figures 4 and 5 show spring-summer salvage at south Delta pumps for 2000 and 2016, respectively. Again, much higher salvage in 2000 reflects the order of magnitude greater abundance in 2000 than in 2016.

Delta Smelt

Delta Smelt continue to be virtually extinct in the Bay-Delta. Figures 6 and 7 show abundance and distribution in 2000, the last near normal abundance year (pre-Pelagic Organism Decline), and 2016, respectively. Figures 8 and 9 show spring-summer salvage at south Delta pumps for 2000 and 2016, respectively. The relatively high salvage in 2000 reflects the general abundance at the end of the 90’s. The fact that there are no longer Delta Smelt in the 2016 Townet Survey or in salvage is a very clear indication that Delta Smelt are virtually extinct. The July experiment, though well intended, was a little too late.

Figure 2. Striped Bass catch per 10,000 cubic meters in June 2000.

Figure 3. Striped Bass catch per 10,000 cubic meters in June 2016.

Figure 4. South Delta salvage of Striped Bass May-July 2000.

Figure 5. South Delta salvage of Striped Bass May-July 2016.

Figure 6. Delta Smelt catch per 10,000 cubic meters in June 2000.

Figure 7. Delta Smelt catch per 10,000 cubic meters in June 2016.

Figure 8. South Delta salvage of Delta Smelt May-July 2000.

Figure 9. South Delta salvage of Delta Smelt May-July 2016. (Salvage was zero.)

Experiment – Part 2 Yolo Bypass Flow

Posted on July 30, 2016 by Tom Cannon

Recently I posted about an unprecedented experiment being undertaken as part of the State’s new Delta Smelt Resiliency Strategy July 2016. That experiment now underway (“Experiment 1”) involves increasing Delta outflow in the latter part of July, 2016. The Strategy also included the North Delta Food Web Adaptive Management Projects (“Experiment 2”), management actions that would benefit juvenile and sub-adult Delta smelt by enhancing the north Delta forage supply for Delta smelt. Experiment 2 involves enhancing flow through the Yolo Bypass to the north Delta by closing the Knights Landing Outfall Gates and routing water from the Sacramento River at Hamilton City (GCID intakes) via the Colusa Basin Drain system into the Yolo Bypass to promote food production in areas where Delta smelt are known to occur. The objective of Experiment 2 is to enhance flow and increase nutrient inputs into the tidal north Delta in the Cache Slough-Lower Bypass region. Future food web enhancement flows would also be considered for “additional months in ways that will not conflict with agricultural and waterfowl management actions based on the availability of water to augment flows in the Yolo Bypass. DWR will also explore options for increasing outflow from the Yolo Bypass during the spring.” Experiment 2 also commenced in July 2016 as an “Emergency Action to Help Delta Smelt”.

As it turned out, the two experiments were timed together, probably to complement one another. Colusa Basin Drain flows increased in mid-July in Experiment 2 via diversion from GCID intakes at Hamilton City (Figure 1). Delta outflow (Figure 2) was increased in Experiment 1 by reducing Delta exports on July 15. Flow through the Yolo Bypass was increased (Figure 3) by closing the Knights Landing Outfall Gates from the Colusa Basin Drain to the Sacramento River and routing the flow through the Knights Landing Ridge Cut to the upper Yolo Bypass on down to Cache Slough and the North Delta (see route in Figure 1). Net flow through lower Cache Slough (Figure 4) increased from the combined effect of the higher flow in Yolo Bypass and the increased flow through Miners Slough and Steamboat Slough that resulted from reduced exports.

So is Experiment 2 having the desired effects? Water temperature in the upper and lower Bypass continue close to the 80°F mark due to high summer air temperatures, although the water temperature in the lower Bypass’s Tule Canal has been measurably higher than that in the adjacent Ship Channel (Figure 5). The higher flow in the Tule Canal likely carries a high organic load as is evident in the low night-time dissolved oxygen levels of 3 to 5 mg/l (Figure 6). Concentrations of salts (Figure 7) and organic matter (Figure 8) increase in the lower Bypass with higher flow. Plankton productivity as measured by chlorophyll levels in the lower Sacramento River channel at Rio Vista immediately below Cache Slough, though low (<10 micro-grams per liter), shows signs of increasing (Figure 9). However, several miles downstream in the channel at Sherman Island, there has been no sign of an increase in plankton (Figure 10). If an increase is indeed real, it is not clear if it is being caused by the higher Delta outflow, lower Delta exports, higher flow in the Bypass, or some combination thereof.

All in all, the warm nutrient- and organic-laden 500-600 cfs of water from the Colusa Basin agricultural drain moving down the Bypass appears to reach the tidal lower Bypass/Cache Slough complex. There, it mixes with higher net and tidal flows of Cache Slough and the Sacramento River. With 80,000 to 100,000 cfs going back and forth during the twice daily tide cycle between Cache Slough and Rio Vista, the Colusa Basin water from the Yolo Bypass is quickly mixed, and its signature is lost. The key question: is there sufficient “fertilizer” and extra plankton in this foreign water to stimulate plankton food production in the lower Yolo Bypass, Cache Slough and the north Delta to benefit Delta smelt? A reduction in river flow at Hamilton City from Experiment 2 might be considered an impact to Sacramento River fish unless additional water is specifically released from Shasta Reservoir for the experiment, or unless GCID water contractors forgo use of a portion of their allocated diversion at Hamilton City.

At a minimum, Experiment 2 has proved the efficacy of an action that might be even more effective from late fall to early spring when water used to stimulate plankton production in the Delta would augment the benefits of cooler, higher flows in the Sacramento River.

Figure 1. Path of flows diverted from the Sacramento River near Hamilton City. Water will move down through GCID’s system, into the Colusa Basin Drain and Knights Landing Ridge Cut, through Wallace Weir and the Yolo Bypass, and into the Delta near Rio Vista. Source: http://www.norcalwater.org/wp-content/uploads/Smelt-action-fact-sheet..pdf