In an earlier post, I suggested “spill” to help recover salmon in the Central Valley. Spill is nomenclature used for reservoir releases. In this case I refer to spill as reservoir releases to help juvenile salmon emigrate from spawning reaches below dams to the ocean. On the Columbia River, “spill” refers to reservoir releases around hydropower turbines usually through spillways. Such spills have been used successfully on the Columbia River to avoid turbine passage that may kill young salmon and to create flows through and below reservoirs to reduce young salmon mortality by shortening their emigration time. On the Sacramento and other Central Valley rivers, “spill” releases can go through hydropower turbines because young salmon start their emigration below the dams. Young salmon have been found to emigrate during flow pulses, with survival directly related to the amount of flow.

More “spill” below the rim dams is needed in the Central Valley to increase survival of naturally produced (wild) salmon and steelhead. Spills help young salmon emigrate from tailwater spawning and rearing reaches below dams to the Delta, Bay, and ocean. Both timing and magnitude are important. Timing relates to when the young salmon are ready to migrate and to natural flow pulses in the Valley. Magnitude is simply how much flow, which relates to precipitation and available reservoir storage supply.

Timing

Most of the Chinook salmon runs emigrate to the San Francisco Bay-Delta as fry soon after hatching. Some migrate as sub-yearling fingerlings and smolts¹ while a few migrate as yearling smolts.

Winter Run Salmon

Winter Run hatch in late summer and early fall in the Sacramento River below Shasta and Keswick reservoirs. They usually emigrate as fingerlings and pre-smolts to the Delta when the river cools, especially during the first flow pulses in late fall and early winter. In drier years they may not emigrate until February or even March. Generally they move down to the Delta in the first flow pulse in December (Figure 1).

Late Fall Run Salmon

Late Fall Run also hatch in winter in the Sacramento River below Shasta and Keswick reservoirs. They usually emigrate as yearling smolts in late fall or early winter, at the same time as the Winter Run. Unlike Winter Run, they are often fully developed smolts and thus migrate quickly to the ocean.

Spring Run Salmon

Spawned in early fall, Spring Run hatch and migrate as fry and fingerlings with the first pulse of flow in late fall and early winter. Some migrate as presmolts and smolts in spring.

Fall Run Salmon

Spawned in fall, Fall Run hatch and emigrate as fry in winter during flow pulses. Some emigrate as fingerlings and pre-smolts in spring.

Figure 1. Older Juvenile Catch Index for the Knights Landing rotary screw trap October through March 2000-2003. Older juveniles are generally Winter Run and Late Fall Run. (Source: http://www.science.calwater.ca.gov/pdf/ewa/support_docs_110804/ Salmon%20Criteria%20Figures%201_2_Chappell.pdf)

Steelhead

Steelhead spawn in winter and spring and emigrate as smolts after rearing in Valley rivers for one to three years. They migrate to the ocean during winter and spring flow pulses.

Spill Recommendations

To illustrate my recommendations, I focus on 2015 – a drought year with very limited reservoir supply and managed spill potential. Such years would be considered worst case scenarios for applying spill prescriptions. Yet despite limited potential in 2015, there were opportunities with the available supplies and precipitation to provide spill that would have substantially benefited salmon. Below are charts of flows for drought water year 2015 that depict the effects of two storm periods on Delta inflow and outflow. Delta inflow came primarily from runoff in un-dammed tributaries. Figure 2 depicts Delta inflow at Freeport with two distinct pulses of storm flow. These same flow pulses are apparent as Delta outflow to the Bay in Figure 3.

Figure 2. Delta inflow in water year 2015. (Source: CDEC)

Figure 3. Delta outflow in water year 2015. (Source: CDEC)

Below Shasta-Keswick in the lower Sacramento River, there was no winter storm flow (Figure 4). There were only two small managed flow increases of about 1000 cfs for three or four days each (a total of about 15,000 acre-ft), because Shasta held nearly all of its inflow from the two storm periods (Figure 5). Shasta inflow reached over 20,000 cfs for six days in each of the storms (Figure 6). Out of approximately 1,500,000 acre-ft of new storage inflow, Reclamation released only15,000 acre-ft (1%) of storm inflow for salmon.

A spill prescription of just 5% of inflow below Shasta-Keswick in the primary nursery for Winter Run salmon could have provided an increased 3000-4000 cfs of “spill” for seven days, instead of the 1000 cfs increases. Instead of going into the irrigation season at 2.72 million acre-ft, in storage, Shasta would have started at 2.67 million acre-ft. Given the potential benefit of the flow releases, this prescription even for a drought year is more than reasonable.

This example is for the fourth year of drought, when the reservoir began the winter at only 25% of capacity. In wetter years when storage is over 50% capacity, spills of 10% should be considered.

The same circumstances and potential benefits occur below other large Central Valley storage reservoirs, especially Oroville Reservoir on the Feather River and Folsom Reservoir on the American River. Spills of 5% in low storage years and 10% in higher storage years are reasonable prescriptions for their depressed salmon and steelhead populations.

Figure 4. Reservoir releases from Shasta-Keswick in water year 2015. Only two small releases were made in the storm periods.

Figure 5. Shasta Reservoir storage in water year 2015. The two storm periods added nearly 1.5 million acre-feet of water to the reservoir.

Figure 6. Shasta Reservoir inflow in water year 2015.

Klamblog¹ recently reported that the Scott River Chinook salmon are again delayed from ascending the lower Scott from the Klamath River because of low water flow. This major Klamath tributary to the west of Mt. Shasta and Weed, CA that flows most winters with thousands of cubic feet per second (cfs) from rain and snow from the Trinity and Marble mountains has been flowing at less than 10 cfs this summer and fall. The salmon simply cannot migrate up this large, steep river with such low flow, especially in dry years when there is no snowmelt after June. The salmon simply wait for rain at the mouth of the Scott. Rains often come by December, just in time for California’s last viable run of Coho salmon, but too late for the Chinook.

As usual the blame is on irrigators in Scott Valley who draw down the water table with heavy groundwater pumping and surface water diversions in the summer for hay and pastures. The State Board did restrict most surface diversions this summer, but with little snowpack there was little streamflow to restrict. Scott Valley often has high groundwater, but with little snowpack recharge, less flood irrigation, and heavy pumping, groundwater seepage and ag returns to the river have virtually ceased, leading to the low flows.

Surprisingly, there is a solution that ranchers are willing to do – pump groundwater into the river in the fall after the summer irrigation season. There is more than enough pumping capacity and groundwater available. Ranchers only want payment for the electricity – a reasonably modest cost. In years like this we are talking about 8 to 10 weeks of a nominal amount of pumping and groundwater storage with a high likelihood that the groundwater used would be replaced/recharged this coming winter and spring.

The concept and proposal have fallen on deaf ears, and the ranchers have circled their wagons much like the salmon in the video link below. As the political fight over water goes on, we should take every opportunity like this one to save the salmon from extinction.

This is the last of four part series on the effects of the Shasta-Trinity Division on Sacramento and Klamath-Trinity River salmon. Part 1 introduced the problem: the failure of Reclamation to manage the Shasta-Trinity Division to protect the salmon resources of the Sacramento and Klamath-Trinity river systems. Parts 2 and 3 summarized the effects on salmon in the Sacramento River and Klamath-Trinity, respectively. In part 4, we suggest solutions to the problems.

The Reasonable and Prudent Alternative (RPA) in the NMFS 2009 Biological Opinion (NMFS OCAP BO) for operation of the federal Central Valley Project (CVP) and the State Water Project (SWP) simply does not go far enough to protect salmon resources affected by the Shasta-Trinity Division of the CVP. NMFS has concluded the RPA is all it can order, acknowledging that it is not enough in the driest years. But even in the worst years, there is much that could be reasonably done to save the salmon in both river systems, including action under Reclamation’s control and NMFS’s jurisdiction.

NMFS’s Biological Opinion states: “NMFS recognizes that the RPA must be an alternative that is likely to avoid jeopardizing listed species or adversely modifying their critical habitats, rather than a plan that will achieve recovery.”¹ However, the RPA is not adequate to avoid jeopardy because the two long-term elements (reintroduction above Shasta and restoring Battle Creek) are too slow in developing. NMFS has also failed to petition the State Board to modify Water Right Order WR-90-05 to limit deliveries to Sacramento Valley Settlement Contractors in drought years, a need described in the BO. Continuing deliveries to the Settlement Contractors in summer of 2014 led directly to the loss of the 2014 Winter Run brood year.

“Providing fish passage at Shasta, Nimbus, and Folsom Dams, which ultimately is the only means of counteracting the loss of habitat needed for egg incubation and emergence, and steelhead over-summering habitat at lower elevations. This habitat loss has already occurred and will be exacerbated by climate change and increased water demands”. Habitat and CVP operations were adequate in the early 1970s, 30 years after Shasta Dam was constructed to sustain the Winter-Run population at 40 to 50 thousand spawners each year. It is the conditions below the dams that have changed to make sustaining salmon more difficult. Many of the effects are reversible through CVP operation changes and restoration of habitats below the dams. It was just over a decade ago the population had again reached 20,000 under the concerted funding and management afforded by the CVPIA and prescriptions of the previous NMFS BO.

“The effects analysis in this Opinion highlights the very challenging nature of maintaining an adequate cold water pool in critically dry years, extended dry periods, and under future conditions, which will be affected by increased downstream water demands and climate change. This suite of actions is designed to ensure that Reclamation uses maximum discretion to reduce adverse impacts of the projects to winter-run and spring-run in the Sacramento River by maintaining sufficient carryover storage and optimizing use of the cold water pool.” Reclamation has not used maximum discretion, and thus has not maintained sufficient carryover storage in Shasta or Trinity reservoirs and has failed miserably at managing the cold-water pools in both reservoirs.

There are many instances where Reclamation has misrepresented its abilities and intentions and has inadequately portrayed its underlying reasons for taking specific actions in the operation of the Shasta-Trinity Division. Its primary objective has been to meet the water demands of contractors and to generate the maximum amount of peaking power possible from the Division’s many hydropower plants.

“The effects analysis in this Opinion, and supplemental information provided by Reclamation, make it clear that despite Reclamation’s best efforts, severe temperature-related effects cannot be avoided in some years. The RPA includes exception procedures to deal with this reality. Due to these unavoidable adverse effects, the RPA also specifies other actions that Reclamation must take, within its existing authority and discretion, to compensate for these periods of unavoidably high temperatures. These actions include restoration of habitat at Battle Creek that may be support a second population of winter-run, and a fish passage program at Keswick and Shasta dams to partially restore winter-run to their historical cold water habitat.” The severe temperature related effects on the Sacramento and Klamath-Trinity rivers can be avoided by better balancing the water supply between contractor water demands, peaking power generation, and salmon.

The BO allows sustaining Winter Run spawning to only the 5-mile reach between Redding and Keswick Dam in drought years like 2014 and 2015. Even in these years salmon were not protected in this minimal reach. (Map Source)

“An RPA must avoid jeopardy to listed species in the short term, as well as the long term.   Essential short-term actions are presented for each division and are summarized for each species to ensure that the likelihood of survival and recovery is not appreciably reduced in the short term (i.e., one to five years).  In addition, because the proposed action is operation of the CVP/SWP until 2030, this consultation also includes long-term actions that are necessary to address project-related adverse effects on the likelihood of survival and recovery of the species over the next two decades.”   The RPA prescribed in the NMFS BO obviously is inadequate to avoid jeopardy especially in the short term.  The following are further actions necessary to avoid jeopardy.

Reduce Reservoir Releases Designed to Meet Contractor Water Demands

Reclamation, NMFS and the State Board must reduce Shasta and Trinity reservoir releases to meet downstream water demands.  They have instead adopted the illegal and ineffective strategy of  weakening standards to satisfy demands during the present four-year drought, and salmon have gone unprotected.  Redistribution of water demands via use of spring and fall water transfers in the Central Valley has generally aggravated the problem by adding to water demands from August through November when cold water pools in reservoirs are limited.  Transfers are a further burden because of the need to add carriage water.  Export of Trinity water to the Sacramento River to meet contractor demands places a burden on both the Trinity and Shasta cold water pools.  Target end-of-September “safe” carryover storage levels have not been achieved in 2014 or 2015 at either Shasta or Trinity reservoirs.

Changes in Hydropower Operations

The Shasta-Trinity Division produces a lot of “green” energy through hydropower.  Having Lewiston and Keswick reservoirs below Trinity and Shasta reservoirs further allows hydro-peaking to meet daily patterns of electricity demands.  The two-step drop for Whiskeytown transfers from the Trinity to the Sacramento adds even more potential peaking power.  Trinity Reservoir water drops from a 2200-2400 ft elevation to 1900-ft at Lewiston Reservoir, to 1200-ft at Whiskeytown, to 600-ft at the Spring Creek Powerhouse on Keswick Reservoir providing a substantial potential for peaking hydropower.

Our analysis of operational data shows that peaking power generation leads to added heating of Lewiston, Whiskeytown, and Keswick reservoirs, and added loss of cold water pools from Shasta and Trinity.  Afternoon peaking generation pulls warmer water into penstocks than nighttime generation.  Generating more at night reduces the loss of cold water pools, but at the expense of the high-value peak power.  No mention of this option is included in the NMFS BO RPA.

The RPA does include Reclamation’s ability to bypass the hydropower systems at both Shasta and Trinity dams and releasing cold water via the lower level outlets.  The option was not employed effectively in 2014 or 2015 at either dam.

Installation of temperature control devices and temperature curtains at reservoir inlets to the hydropower systems has proven beneficial but not totally effective.  Planned improvements should be immediately implemented.  The Shasta Temperature Control Devise proved ineffective in late summer 2014.  The Whiskeytown temperature curtain fails to reduce water temperatures in water released to Keswick Reservoir below 58°F, thus requiring the added release of Shasta cold water pool to meet the 54-56°F required release from Keswick Reservoir to the Sacramento River.

Summary of Potential Measures

Changes in the operation of the Shasta-Trinity Division of the Central Valley Project in the following are necessary to preserve Sacramento and Trinity River salmon:

1. Provide a better balance between water supply demands, hydropower production, and salmon needs.
2. Improve management of reservoir storage, especially the amount of cold-water pool in reservoir storage
3. Better manage the distribution of reservoir releases between power turbines (warmer) or lower level bypasses (colder)
4. Improve the daily pattern of reservoir releases to meet peaking power demands for electricity while minimizing demands on reservoir coldwater pools.
5. Improve blending capabilities in reservoir outlets to power turbines (Shasta has a Temperature Control Devise that allows pulling water from different lake levels)
6. Improve water temperature mixing in the two re-regulating reservoirs (Keswick below Shasta and Lewiston below Trinity)
7. Improve water temperature management of releases to the Sacramento and Trinity Rivers (do not relax water temperature standards)
8. Better manage the export of Trinity Reservoir water via Lewiston and Whiskeytown reservoirs to Keswick Reservoir (to Sacramento River) to minimize the use of Shasta’s cold water pool to cool water originating in the Trinity .
9. Truly address the NMFS BO RPA goals and objectives for the near-term:

“In the near term, adverse effects of project operations to winter-run will be reduced primarily through the following measures:  Modifications to Shasta reservoir management will result in more reliable provision of suitable water temperatures for spawning and egg incubation in the summer months.  The new year-round Shasta management program is expected to minimize frequency and duration of temperature related egg mortality in dry and critically dry years, thus reducing, though not eliminating, the population level stress of these temperature related mortalities.  The new Shasta program will allow for an expanded range of habitat suitable for spawning and egg incubation in wetter year types (i.e. through meeting downstream compliance points more often).  Over time, this will help to preserve diversity of run-timing and decrease the risk of a single event in a localized area causing a population level effect.  Temperature related effects on winter-run will persist into the future, and cannot be fully off-set through Shasta reservoir storage actions, due to physical and hydrological constraints on the CVP system, and the delivery of water to non-discretionary CVP contractors (e.g. Sacramento River Settlement Contractors).  Given a fixed supply of cold water in any given year starting in May, as an overall strategy, the RPA prioritizes temperature management in favor of winter-run due to their endangered status and complete dependence on suitable habitat downstream of Keswick for their continued survival.”

This is part 2 of a four-part series on the effects of the Shasta-Trinity Division on Sacramento and Trinity-Klamath salmon. Part 1 is an introduction to the series. Part 2 is a discussion of the effects of the Shasta-Trinity Division on Sacramento River salmon.

There are two key points regarding the Winter-Run Chinook Salmon of the Sacramento River in the 2009 NMFS Biological Opinion (BO) that address the long-term operation of the Shasta-Trinity Division:

•  “The current status of the affected species is precarious, and future activities and conditions not within the control of Reclamation or DWR are likely to place substantial stress on the species.” It turns out that Reclamation also added a lot of stress that was under their control in both 2014 and 2015 that has put the species under extreme jeopardy.
•  Simply altering project operations was not sufficient to ensure that the projects were likely to avoid jeopardizing the species or adversely modifying critical habitat. So NMFS prescribed some long term actions (i.e. trap and hauling salmon above Shasta and establishing a Winter Run population in Battle Creek). Because these solutions remain far off, and short-term project operation prescriptions have been entirely ineffective in sustaining the population in the interim, the Winter Run population is in dire straits¹.

NMFS’s near-term measures prescribed in the BO focused on providing suitable water temperatures in the Sacramento River below Shasta in a high percentage of years. The BO prescribed fewer and fewer protections in the drier years with poorer and poorer spawning and rearing habitat near Redding, reaching an unintended consequence of little or no viable habitat left in late summer 2014 and sub-marginal habitat through the summer of 2015. NMFS blamed poor reservoir temperature modeling and forecasting by Reclamation in both years. In reality, problems in both years could have been avoided.

The basic problem in 2014 and 2015 was that the operation of the Shasta-Trinity Division resulted in elevated water temperatures that had lethal and sub-lethal effects on egg incubation and juvenile emergence in the upper Sacramento River. Their excuse: “The immediate operational cause was lack of sufficient cold water in storage to allow for cold water releases to reduce downstream temperatures at critical times and meet other project demands.” The real problem was defective forecasting tools and over-allocation of water to contractors during the third and fourth years of the drought. The lethal outcome was also not only the result of high water temperatures, but also of redd stranding from flow reductions (see figure below).

CDFW Report on stranding mortality of salmon eggs and alevins in the Sacramento River in late summer 2014. It is obvious from the report’s cover photo that the problem was not just water temperature.

NMFS’s “Reasonable and Prudent Alternative (RPA)” in its Biological Opinion

“NMFS made many attempts through the iterative consultation process to avoid developing RPA actions that would result in high water costs, while still providing for the survival and recovery of listed species. … We will seek to incorporate this new science as it becomes available through the adaptive management processes embedded in the RPA.” The RPA requires Reclamation to seek higher water costs (more water for salmon) from the State Water Resources Control Board in extreme conditions. But in 2014 and 2015, Reclamation instead asked the State Board for the opposite: contracted deliveries to senior water contractors at the expense of the fish, with a simultaneous weakening of water quality standards for flow and water temperature. The Board granted Reclamation’s request, with NMFS’s “concurrence.” In both its Biological Opinion and in real time decision making, NMFS limited water costs but failed to protect the species. A Biological Opinion can only work when a regulated entity follows it and a regulator enforces it.

RPA Action 1.1.4

The RPA included Action I.1.4, Spring Creek Temperature Control Curtain Replacement. The curtain in Whiskeytown Reservoir at the inlet to the Spring Creek Powerhouse on Keswick Reservoir was replaced in 2011; however, the curtain was minimally effective in cooling water transferred to the Sacramento River from Trinity Reservoir. Large volumes of Shasta cold-water pool (50°F) had to be released into Keswick Reservoir to cool warmer (58-59°F) Spring Creek Powerhouse releases to keep releases to the Sacramento River at the required 54-56°F.

RPA Action Suite 1

The RPA also includes a suite of actions for operating the Shasta-Trinity Division.

1. “Ensure a sufficient cold water pool to provide suitable temperatures for winter-run spawning between Balls Ferry and Bend Bridge in most years, without sacrificing the potential for cold water management in a subsequent year. Additional actions to those in the 2004 CVP/SWP operations Opinion are needed, due to increased vulnerability of the population to temperature effects attributable to changes in Trinity River ROD operations, projected climate change hydrology, and increased water demands in the Sacramento River system.” In 2014 and 2015 water temperatures downstream of Redding, including the reach between Balls Ferry and Bend Bridge, were lethal to Winter Run eggs and alevins. The NMFS BO and in particular this RPA action suite were simply not followed. Instead, NMFS “concurred” with relaxing the water quality standards that resulted in objectives not being met.
2. “Ensure suitable spring-run temperature regimes, especially in September and October. Suitable spring-run temperatures will also partially minimize temperature effects to naturally-spawning, non-listed Sacramento River fall-run.” Fall temperatures in the Sacramento River for Spring Run salmon were also lethal in 2014. It is unclear at present whether sufficient cold-water pool will be available in the fall of 2015 to prevent a repeat of 2014.

RPA Action 1.2.4

May 15 through October Keswick Release Schedule (Summer Action)

1. “Reclamation shall develop and implement an annual Temperature Management Plan by May 15 to manage the cold water supply within Shasta Reservoir and make cold water releases from Shasta Reservoir and Spring Creek to provide suitable temperatures for listed species, and, when feasible, fall-run.” The 2014 and 2015 plans proved faulty in their forecasts for sustaining the cold water pool in Shasta, and thus this requirement was not met even in the 9 mile reach of the Sacramento River immediately downstream of Keswick Reservoir.
2. “Reclamation shall manage operations to achieve daily average water temperatures in the Sacramento River between Keswick Dam and Bend Bridge as follows: Not in excess of 56°F at compliance locations between Balls Ferry and Bend Bridge from May 15 through September 30 for protection of winter-run, and not in excess of 56°F at the same compliance locations between Balls Ferry and Bend Bridge from October 1 through October 31 for protection of mainstem spring run, whenever possible.” Reclamation, the State Board, and NMFS found maintaining these objectives impossible in 2014 and 2015.

Unable to meet temperature requirements, Reclamation and NMFS are seeking “other solutions”:

1. Expansion of the Livingston Stone National Fish Hatchery production for Winter-Run from the typical broodstock of 120 adults to accommodate up to 400 adults.
2. Restrictions on recreational and commercial fishing to benefit of Winter-Run salmon.
3. The agencies will continue to actively investigate other project elements that make sense, including:
   • applying reflective paint or other shading on the penstocks into Whiskeytown Reservoir
   • accelerating acquisitions related to the installation of the Oak Bottom Temperature Curtain in Whiskeytown Reservoir,
   • decreasing the exposure of cold water from Trinity to sunlight as it travels through the powerhouse and exposed pipes that to help ensure this cold water remains cold.
   • continue to seek input from stakeholders to develop other non-flow actions that may help minimize overall impacts (e.g. , predation control strategies and/or restoration, hatchery, etc.)²

The demise of 2014 Winter Run brood year has been attributed to high water temperature in the Sacramento River below Keswick Reservoir in late summer 2014.

Another contributing factor to the 2014 brood year demise was high flows during spawning (June-July) followed by low flows at emergence (September).

The reduction in inflow from the Trinity in 2014 contributed to Winter Run redd dewatering and higher water temperatures in the Sacramento River near Redding in 2014.