Author Archives: Tom Cannon

Stanislaus Trout (Steelhead)

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An August 18, 2016 article in the Calaveras Enterprise (“Trout population plummets”) and an August 15, 2016 post on the Fishbio blog describe a recent decline in numbers of trout in the lower Stanislaus River. Fishbio pegged the cause of the problem on to four years of drought and to the fact that the Bureau of Reclamation allowed New Melones Reservoir to fall in storage so far as to lose its cold water pool needed for trout production. As reported in the Enterprise, the Oakdale Irrigation District and South San Joaquin Irrigation District issued a statement arguing that “flawed science” in the National Marine Fisheries Service’s 2009 biological opinion issued for the operation of the Central Valley causes federal dam operators to release water in ways that do not benefit steelhead and trout. The Enterprise quotes the Districts as stating: “The current flow standards are destroying the fisheries that they are intending to protect and doing so at the expense of Central Valley agribusiness and urban interests, who also depend upon a healthy and sustainable river.” 

The irrigation districts would prefer that the water released for fish be allocated instead to their constituents. Lost in the discussion is the notion that reducing river flows is not the only way to maintain storage levels in New Melones Reservoir. If the irrigation districts had taken less water over four years of drought, the cold water pool in New Melones could have ended up, in 2015, in much better shape. But the Districts lay the decline of “trout” at the feet of the biological opinion. The fish flow prescriptions biological opinion are not designed for “trout.” They are designed for steelhead migration to the Bay-Delta and ocean. The biological opinion prescribes multi-day spring pulses in flow up to several thousand cubic feet per second to stimulate steelhead (and juvenile salmon) emigration toward the ocean. It states in part:

Objective: To maintain minimum base flows to optimize CV steelhead habitat for all life history stages and to incorporate habitat maintaining geomorphic flows in a flow pattern that will provide migratory cues to smolts and facilitate out-migrant smolt movement on declining limb of pulse. 1

Steelhead need stimulus to migrate. They need the benefits of higher velocities and more turbid water to migrate successfully. Without stimulus, potential steelhead will stay and become resident trout. Mother Nature has given them the inherent knowledge that to go without the flow is to die along the way.

Flow in the Stanislaus River is controlled by operations of New Melones Reservoir (Figure 1). The premise of the article and post is that reservoir drawdown from pulsed flow releases caused the high water temperatures in the lower Stanislaus River that resulted in high trout mortality and the low numbers of trout observed in the snorkel surveys. There is no doubt that low reservoir levels led to warmer water being released into the lower Stanislaus from Goodwin Dam. The information presented in the Fishbio post and report shows clearly that water temperatures were 5 to 10°F higher than normal in the lower Stanislaus, reaching the stressful level of 65°F or even higher downstream of Goodwin Dam at Orange Blossom Bridge (Figure 2). The water temperature criteria prescribed in the biological opinion for the summer at Orange Blossom Bridge is 65°F. The reservoir did fall dangerously low in 2015 (Figure 3).

Figure 1. Map of lower Stanislaus River with USGS gaging stations.

Figure 1. Map of lower Stanislaus River with USGS gaging stations.

Figure 2. Daily average water temperature (°F) in the lower Stanislaus River at Orange Blossom Bridge 2011-2016

Figure 2. Daily average water temperature (°F) in the lower Stanislaus River at Orange Blossom Bridge 2011-2016

Figure 3. New Melones Reservoir storage in acre-feet 2011-2016.

Figure 3. New Melones Reservoir storage in acre-feet 2011-2016.

The Fishbio report relates that water temperature becomes a problem when summer storage falls into the 300-500 thousand ac-ft range.  It would also appear that levels of 500-600 thousand acre-feet, such as those that occurred in summer 2014 and 2016, also lead to elevated water temperatures based on a close look at Figures 2 and 3.

A factor not mentioned by Fishbio is that streamflow in the lower Stanislaus in summer 2015 was lower in 2015, 150-200 cfs, compared to 200 cfs or higher in other summers of the 2011-2016 period (Figure 4).  Such lower flows can also contribute to higher water temperatures.  Lower flows can also affect “trout” survival by significantly reducing rearing space and quality.

A factor that Fishbio did mention was a possible “increase in downstream migration.”  After all, the flow pulses were prescribed to stimulate steelhead smolt emigration.  Flow pulses in combination with higher water temperatures may have stimulated outmigration resulting in lower total numbers.

The main theme of the irrigation districts and Fishbio is that by not providing the pulse flows in spring, it would save up to 100 thousand acre-feet of storage, thus keeping the reservoir higher and water temperatures lower in the river below.  But again, what is missing from the discussion is the effect of reservoir operation on the whole process, and especially on storage.  That effect can be seen in Figures 5a and 5b.  The natural flow regime is highly modified.  The natural winter high flows are retained by the reservoir and released in spring and summer.  Releases to irrigators from storage in 2015 over the April – September irrigation season amounted to approximately four hundred thousand acre-feet (see Figure 3), most of which came from storage carried over from previous years, which made up much of the cold water pool.  This repeated the pattern of previous years, when in fact deliveries to the districts were even higher.  With so little water left in storage by 2015, the districts had no one left to take water from but the fish.

Figure 4. Daily average streamflow (cfs) in the lower Stanislaus River at Orange Blossom Bridge from 2011-2016.

Figure 4. Daily average streamflow (cfs) in the lower Stanislaus River at Orange Blossom Bridge from 2011-2016.

Figure 5. New Melones Reservoir inflow (blue line) and outflow (orange line) in water year 2015 (top) and 2016 (bottom). Note prescribed fall and spring pulse flow releases for salmon and steelhead.

Figure 5. New Melones Reservoir inflow (blue line) and outflow (orange line) in water year 2015 (top) and 2016 (bottom). Note prescribed fall and spring pulse flow releases for salmon and steelhead.

Low San Luis Reservoir

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Tim Quinn, Executive Director of the Association of California Water Agencies (ACWA), is trying again, as in so many of his blog posts, to hornswoggle us into believing that many of this year’s water woes have been caused by “overzealous” fish protections.1 His August 17, 2016 post on the Association of California Water Agencies (ACWA) website is focused on why San Luis Reservoir in the San Joaquin Valley has such low water storage this summer. San Luis storage went from 50% of capacity at 1 million acre-feet (MAF) at the beginning of April to 0.2 MAF (10% of capacity) at the beginning of August. All to human use.

Mr. Quinn correctly points out that lack of federal Delta exports to San Luis was due to a concerted effort by the Bureau of Reclamation to conserve Shasta Reservoir’s storage and cold-water pool to save this year’s spawn of winter-run salmon in the Sacramento River below Shasta. In 2016, federal and state agencies were gravely concerned about protecting this year’s spawn of winter-run salmon below Shasta. The past two years’ spawns had been wiped out after Shasta ran out of cold water. So after Shasta filled and spilled in late March, releases to the Sacramento River were limited to retain Shasta’s cold-water pool to sustain salmon through the summer (Figure 1). Releases (Shasta reservoir outflow) from the first of April through the end of July were about 700,000 acre-feet less than normal, saving reservoir storage and the cold-water pool. Instead of falling to 2.9 (MAF) of storage (64% of capacity) at the end of July as would more typically have been the case, Shasta was drawn down only to about 3.6 MAF (80% of capacity).

Figure 1. Sacramento River flow below Shasta/Keswick reservoirs near Redding. Red lines depict normal-release-pattern river flows at Redding.

Figure 1. Sacramento River flow below Shasta/Keswick reservoirs near Redding. Red lines depict normal-release-pattern river flows at Redding.

But there is more to the story. Sacramento Valley water contractors still took their normal allotments from the reduced Sacramento River supply, leaving little for San Luis. State Water Project contractors exported near the maximum from their Delta diversion facilities at Clifton Court this summer, using Oroville Reservoir water, while federal exports were less than 50%. Federal Folsom Reservoir water was used for Delta outflow requirements so that State Water Project exports could be accomplished (the feds owed the state water from 2015). Folsom, which started the year nearly full at 850 TAF, is now only at 40% of capacity and has once again closed its marinas. Ironically, enough water has flowed from the Delta this summer to (State Water Contractor) Metropolitan Water District’s Diamond Valley Reservoir in southern California to allow the Met to open its Diamond Valley marinas.

Just to be equitable, Mr. Quinn doesn’t blame only the salmon. He also blames the San Luis problem on the fact that “federal officials over-cautiously kept [Delta] pumping levels very low to protect Delta smelt” during winter storm pulses (Figure 2). He correctly states that restrictions on the federal and state water projects in the biological opinion for Delta smelt kept winter exports from the Delta at 20-70% of capacity. But again, where’s the context? Project operation in 2014 and 2015 just about obliterated the last remnant Delta smelt, and the some of the few pesky smelt that survived were indeed found to be spawning in the central Delta, not far from the export pumps, during the winter. Before we throw around adverbs like “over-cautiously,” perhaps we should balance with “recklessly” when we talk about what happened to bring us to a situation that demands such caution.

Figure 2. Storm pulses in the last five years from the Sacramento River into the Delta.

Figure 2. Storm pulses in the last five years from the Sacramento River into the Delta.

Mr. Quinn further states:

This scenario underscores the peril of regulatory agencies focusing almost exclusively on species protection at the expense of water supply. Moreover, efforts to protect endangered fish virtually always narrowly focus on a single element – temperature control or flows – while failing to address other important factors affecting the species. Allowing a single-stressor approach to drive water management decisions only serves to maximize conflict between species protection and water supply, while failing to adequately serve either. And we continue to lose water supply every day as a result.

Well, the water is needed by all the fish species, including all six listed species. It is needed for habitat, water quality, and all ecosystem functions in the rivers, Delta, and Bay.

About half of the water that hits the watershed eventually does reach the Bay as Delta outflow in the drier years, primarily during infrequent winter storms (Figure 2). Much of the rest of the outflow is needed to repel saltwater intrusion into the Delta, so that the water in the state and federal canals is not too salty to export. Annual runoff to the Bay ranges from about 5 to 10 MAF in these drier years. The State Water Board’s staff has said that the estuary needs 75% of unimpaired runoff to be healthy.

During winter storm pulses in a year that follows a dry year sequence, about 60-80% of the water (immediate rain and later snowmelt) is captured in Mr. Quinn’s constituents’ Central Valley rim reservoirs for summer use. In 2015, it was even worse: approximately 50% of the inflow to the Delta from the Central Valley in 2015 occurred during two storm periods. Most of the inflow came from undammed streams and local runoff, while the major reservoirs were capturing 80-90% of their inflow.

The big storms carry the offspring of salmon, steelhead, and sturgeon to the Bay, and represent most of the Bay’s freshwater inflow for the year. With the reservoirs capturing most of the inflows in the really bad years like 2015 , the rivers downstream of the major reservoirs, streams like the Sacramento, Feather, America, Mokelumne, Stanislaus, Tuolumne, Merced, and San Joaquin, get little winter water for fish spawning, rearing, and migrations.

The flow in rivers, the Delta, and the Bay directly or indirectly controls or partially controls all the stressors affecting the listed species. Flow even controls the water districts’ favorite stressor, predation.

Now, Mr. Quinn and his colleagues want us to pay untold billions of dollars for the California “Waterfix,” so they can take more water, especially during the infrequent storms in dry year winters. In the two storm pulses in winter 2015, the WaterFix Tunnels could have been operating at near capacity for about 30 days to take an added approximately 500 TAF, or about 20% of the total from the two storm pulses of Delta outflow. Instead of half the Valley inflow reaching the Bay, only 40% would make it due to the new Tunnels.

Green Sturgeon Status – late summer 2016

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Young green sturgeon captured in Red Bluff trap. This specimen is quite large as most of the green sturgeon caught in the screw traps in late spring and early summer average one inch in length. Source .

Young green sturgeon captured in Red Bluff trap. This specimen is quite large as most of the green sturgeon caught in the screw traps in late spring and early summer average one inch in length. Source1 .

In an August 15, 2016 post on its Pacific Southwest Region website, the US Fish and Wildlife Service observed that the numbers of young green sturgeon have gone up this year in trap collections below the Red Bluff Diversion Dam.2 The article notes that this could represent an increase in the population. Joe Heublein, NMFS’s Green Sturgeon Recovery Coordinator, is also cautiously optimistic, according to the article.

Since 2012, gates at the Red Bluff dam have not hindered adult sturgeon from moving upstream past the dam to reach spawning grounds. Since 2016 was the first non-drought year since 2012, it seems likely that there should be an increase in the capture of recently spawned juveniles migrating downstream past the dam.

Missing from the story, however, is the fact that these juvenile sturgeon faced a particularly tough journey between Red Bluff and the Bay this summer, as discussed in my previous post on green sturgeon. Low flows and high water temperatures were a serious problem for the young sturgeon in the lower reaches of the Sacramento River in 2016. Unless their downstream rearing and migratory habitat is improved, the green and white sturgeon populations will have a bleak future.

The presence of young is a good sign. The species is long-lived, and thus it is not too late to recover this state and federally listed endangered fish. Getting rid of the Red Bluff diversion Dam five years ago was a big first step. The focus now should be on late spring through summer Lower Sacramento River habitat.

Since the beginning of summer 2016, conditions have improved (Charts 1 and 2). In August, flows at Wilkins Slough increased to 5000-7000 cfs, and water temperatures were down near 70°F. In late May and June, water temperatures at Red Bluff (Chart 3) were near lethal (68°F) for the really small fish, and were most likely worse not far downstream (Chart 2). Now temperatures are closer to the Basin Plan’s prescribed 56°F at Red Bluff and 68°F at Wilkins Slough.

The initial problem this year was the result of reduced releases from Shasta Reservoir to save its cold water pool for winter-run salmon, combined with normal agricultural water allocations in the Sacramento Valley. Recent improvements are the result of the normal late summer reductions in irrigation demands. In the future, Basin Plan objectives should be met by a reduction in Sacramento Valley water allocations when water is not sufficient to allow higher overall summer reservoir releases from Shasta.

Chart 1. River flow at Wilkins Slough (RM 125) late spring through summer 2016.

Chart 1. River flow at Wilkins Slough (RM 125) late spring through summer 2016.

Chart 2. Water temperature at Wilkins Slough (RM 125) late spring summer 2016.

Chart 2. Water temperature at Wilkins Slough (RM 125) late spring summer 2016.

Chart 3. Water temperature in Sacramento River at Red Bluff from late spring through summer 2016.

Chart 3. Water temperature in Sacramento River at Red Bluff from late spring through summer 2016.

Low Flows – Deadly Water Temperatures

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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 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 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.

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

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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.