Category Archives: Water Quality

Fall Pulsed Flow Protections for Winter Run Salmon Not in 2017 and 2018

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It is well known that juvenile winter-run salmon migrate downstream to the Delta from their upper Sacramento River rearing area near Redding/Red Bluff with the first fall-winter flow pulses.1 Protection of this critical migration of winter-run has been recommended in recent Delta proceedings. In the WaterFix petitions process at the State Water Resources Control Board, such protection is referred to as “pulse protection.” So based on the importance of protecting winter-run during this key life-history stage, one would think such protection would have been applied in the fall of our most recent wet year 2017 and below-normal 2018. A quick check of the facts indicates otherwise.

In 2017, the initial pulse of juvenile winter-run salmon passed Red Bluff (rivermile 240) during September and October, prior to any flow pulses (Figure 1). The first major pulses of flow occurred in the latter half of November 2017. A migration spike of winter-run-sized smolts at Knights Landing screw traps (rivermile 90) did occur during the flow pulse (Figures 1 and 2). Instead of protecting these winter run as they were entering the Delta, south Delta exports were increased to take advantage of the available inflow (Figure 3). The increase occurred with the Delta Cross Channel partially open (Figure 4), increasing the risks of migrating salmon to south Delta exports. Other than a four-day pulse, Delta outflow generally declined before and after the flow pulse (Figure 5). Salinity in the lower Sacramento and San Joaquin Delta channel generally increased with the higher exports and lower outflows (Figures 6 and 7).

In 2018, the initial pulse of juvenile winter-run passed Red Bluff in September and October prior to flow pulses (Figure 7). The first major pulse of flow occurred at the end of November. A migration spike of winter-run-sized smolts at Knights Landing screw traps occurred during this flow pulse (Figures 7 and 8). Instead of protecting these juvenile winter run as they were entering the Delta, south Delta exports were increased to take advantage of the available inflow, with nearly two-thirds of the Delta inflow being exported (Figure 9).

The lack of protection is likely a consequence of the young salmon not showing up in salvage (Figure 2). For me, the high risk factors are clear.

  1. The lack of salvage simply indicates that few of the migrating salmon survive upon entering the Delta under high exports. High late-November and early-December south Delta exports are a high risk to the juvenile winter-run survival. Traditional high December exports of up to 65% of Delta inflow allowed under D1641 water quality standards are a major risk factor for winter-run salmon that must be changed.
  2. Declining flows below Keswick Dam (rivermile 300) during the fall, combined with the lack of flow pulses, are also a real concern. Juvenile salmon that pass Red Bluff (river mile 240) in September and October are sustained in low flow conditions for nearly 200 miles of modified river channel until the first rains in late November or early December. And the spawning reach directly downstream of Keswick gets no added flow even when it rains, because inflows to Shasta Reservoir are all captured.

For additional information, see agency discussions and data presentations in: http://www.westcoast.fisheries.noaa.gov/publications/Central_Valley/Water%20Operations/Delta%20Operations%20for%20Salmonids%20and%20Sturgeon/DOSS%20WY%202018/winter-run_juvenile_production_estimate__jpe__for_brood_year_2017_-_january_29__2018__1_.pdf

Figure 1. Juvenile winter-run salmon estimated passage and stream flow at Red Bluff (rivermile 240) from late summer 2017 to June 2018.

Figure 2. Lower Sacramento River screw trap collections at Knights Landing (rm 90) since August 2017 along with flow, turbidity, and water temperature. Note late November catch event during flow pulse.

Figure 3. South Delta exports in fall 2017. Note peak exports mid-November through early December – total 10,000-11,000 cfs (22,000 acre-ft per day). Chinook salvage is shown as zero.

Figure 4. Flow through Delta Cross Channel August through December 2017. Note sporadic opening late September through November 2017, and closure at end of November.

Figure 5. Delta outflow August through December 2017.

Figure 6. Salinity (EC) near Rio Vista on lower Sacramento River channel in the Delta, August through December 2017.

Figure 7. Salinity (EC) near Jersey Pt on lower San Joaquin River channel in the Delta, August through December 2017.

Figure 8. Juvenile winter-run salmon estimated passage and stream flow at Red Bluff (rm 240) from late summer 2017 to June 2018.

Figure 9. Juvenile winter-run salmon estimated passage at Knights Landing (rivermile 90) and stream flow at Wilkins Slough (rivermile 125) from late summer to fall 2018. Note early December pulse of fish, flow, and turbidity.

Figure 10. Export rates from two south Delta pumping plants (Tracy TRP and Banks HRO) summer and fall 2018.

Figure 11. Lower Sacramento River flow at Freeport (FPT, rm 55) and Delta outflow (DTO) summer and fall 2018.

Delta Smelt Resiliency Strategy – Update Fall 2018

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A summer pulse flow through the Yolo Bypass via the Colusa Basin Drain (Figure 1) was implemented in September per the Delta Smelt Resilience Strategy’s North Delta Food Web Action (Figure 2). I reviewed the initial application of the action in July 2016, concluding then there was no evidence that the action would meet its overall goals, but that the approach had potential.

The basic concept is this:

– By routing agricultural drain water through Yolo Bypass instead of the Sacramento River, DWR scientists predicted that a flush of plankton-rich water would provide a “seed” for the downstream Delta, enhancing food resources for Smelt. (Note: Historically, summer drain water from Colusa Basin rice fields was discharged into the Sacramento River at Knights Landing.)

– A similar managed flow pulse was generated in July 2016 with the help of Sacramento Valley water users, which helped transport plankton to the Delta. (Note: additional Sacramento River water was diverted near Red Bluff to the Colusa Basin Drain to supplement rice field drainage. There was no evidence that plankton blooms in the Yolo Bypass reach the Delta in meaningful amounts.)

– The action is designed to maximize the environmental benefits of water. Water isn’t “consumed” by the action–it is directed down a different and more productive path to the Delta. (Note: The basic concept is simple. The nutrient-laden drain water stimulates Yolo Bypass productivity, and the added river water flushes it through to the north Delta. Taking some of the Sacramento River at Red Bluff and routing it through the Colusa Basin irrigation and drainage system, then on to the Yolo Bypass tidal channels, should stimulate biological productivity and flush it, along with excess nutrients and organic debris from rice fields into the Delta at the end of the Bypass (Cache Slough – Rio Vista area). The Delta (and smelt) would benefit from the added biological productivity (phyto-zoo plankton) and nutrients (nitrogen, phosphorous, and organic carbon).

Does the concept work, and does it come without complications?

  • During implementation in 2018, there was an 60% uptick in aquatic plant productivity in the lower Yolo Bypass (Figure 3).
  • There was no increase in productivity as of early October in the north Delta at Rio Vista (Figure 4).
  • The water routed through the Bypass was initially warm (>70oF, Figure 5), high in salts (Figure 6), lower in turbidity (Figure 7), and low in dissolved oxygen (Figure 8).
  • Warm water and the high organic load resulted in poor dissolved oxygen levels (3-5 milligrams-per-liter) that violate state standards and are potentially lethal to salmon migrating through the Bypass1.

On a positive note, routing drain water to the Bypass does keep the poor quality drain water out of the Sacramento River below Knights Landing.

In sum, the benefits of the action remain questionable. Waiting to conduct the action until fall when waters are cooler could alleviate high water temperatures and low dissolved oxygen in the water. It might also create more Delta benefits by delaying nutrient use until nutrients reach the Delta. Further research is warranted into the water quality of the drain water, especially its oxygen-depriving, high-organic load and its chemical constituents (salts, herbicides, and pesticides). Otherwise, it may be that the action is little more than an augmentation of the current practice of dumping what might be described as polluted agricultural drain water into Central Valley rivers and the Delta.

Figure 1. Stream flow (cfs) in Yolo Bypass below Colusa Basin Drain outlet. The pulse flow reached the Yolo Bypass on or about August 28 and ended on September 25.

Figure 2. Project scheme and map of key features.

Figure 3. Chlorophyll concentration in lower Yolo Bypass at Lisbon in late summer 2018. There was a 50% increase in late September to about 8 micrograms per liter, although below the target of 10 or higher.

Figure 4. Chlorophyll concentration in north Delta at Rio Vista in late summer 2018. There was a slight decline after September 1 to about 1.25 micrograms per liter, well below the target of 10 or higher.

Figure 5. Water temperature in lower Yolo Bypass at Lisbon in late summer 2018.

Figure 6. Salt concentration (EC) in lower Yolo Bypass at Lisbon in late summer 2018. The drain water entering at the end of August had a high salt concentration.

Figure 7. Turbidity (NTUs) in lower Yolo Bypass at Lisbon in late summer 2018.

Figure 8. Dissolved oxygen (mg/l) in lower Yolo Bypass at Lisbon in late summer 2018. The drop in DO at the end of August reflects the high organic load of the drain water.

  1. Migrating adult salmon are common in the Bypass in September, possibly being attracted to rice drainage flows with the chemical signal of the upper Sacramento River. ↩

Reclamation releases final environmental documents for the Sacramento Deep Water Ship Channel Nutrient Enrichment Project

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A September 24, 2018 Reclamation press release announces:

The Bureau of Reclamation has issued final environmental documents for the Sacramento Deep Water Ship Channel Nutrient Enrichment Project. The project’s purpose is to determine if the addition of nitrogen can stimulate (fish food organisms) production in a section of the ship channel, which is isolated from the Delta in terms of water flow.

The project is an initial step in a broader effort to determine if, through the repair of the West Sacramento lock system, Sacramento River flows could be used to move fish food organisms through the Sacramento Deep Water Ship Channel to the Delta. This step seeks to benefit delta smelt and the Bay-Delta System.

The press release and project Final Environmental Assessment (EA) are misleading in representing existing conditions and future project benefits.

  1. Reclamation fails to explain the high EC (salt levels) in the project reach of the upper ship channel (Figures 1 and 2). Figure 1 includes three black arrows added to the project figure. These arrows represent large municipal/agricultural drains from the adjacent West Sacramento “island basin” that add salts, nutrients, and other wastes to the ship channel on a seasonal basis (generally early spring). The poor productivity in late summer may be at least partially due to these “waste” discharges.
  2. The EA says: “This will restore nitrogen levels that occur naturally earlier in the season before drawdown by phytoplankton growth.” However, high nitrogen levels are not “natural.” They are man-made.
  3. The EA says: “The fertilizer to be used for this experiment contains 1% ammonium nitrogen (NH4-N).” The press release and EA fail to mention billion dollar efforts to remove ammonium nitrate inputs to the north Delta from the Sacramento Regional Wastewater Treatment facility.

The press release acknowledges that repair of the ship channel gates would allow seasonal pulses of high plankton productivity to be flushed into the north Delta. Effective operation of these gates (selective opening and closing) would move existing blooms in the upper Ship Channel down into the Delta, likely eliminating the need for the addition of nitrogen. It would also reduce the temperature of the water in the Ship Channel. For more on these issues, see a previous post.

Figure 1. EA figure of EC (salt) and Chlorophyll levels in ship channel. Added black arrows show West Sacramento drains into ship channel.

Figure 2. EA figure showing consistent high EC levels in upper ship channel.

Record low 2018 juvenile salmon index for fall-run salmon

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In a 9/20/18 Maven’s Science News an article describes a record low index of juvenile salmon from this past winter-spring Red Bluff screw trap survey. The article states that the poor juvenile numbers foreshadow a poor Sacramento River salmon run in 2020. The article is vague as to the cause. The article implies that a likely cause for the poor 2017 adult run and record low 2018 Red Bluff trap index was the trucking of Coleman Hatchery smolts to the Bay during the 2014 drought, which then did not find their way back to Coleman as adults.

The article fails to mention two likely primary causes of the record low index:

  1. Poor rearing and migrating conditions in the lower Sacramento River in winter-spring 2018.1
  2. A 50% reduction in the number of smolts released by the Coleman Hatchery in 2018 (6 million instead of the normal 12 million) from lack of eggs.2

Regardless of the cause, the prognosis for the 2020 run remains grim, as stated in the article. What the article does not forecast is a likely grim forecast for 2018 and 2019. These runs are likely to be low because:

  1. All the Coleman releases in 2016 and 2017 were at the hatchery, with none trucked to the Bay which ensured poor survival of the smolts prior to reaching the ocean;
  2. There were poor juvenile rearing and migrating river conditions in winter-spring in 2016 and 2017,
  3. There were poor spawning run river conditions in summer/fall 2015 and 2016, and
  4. There were poor spawner numbers in 2016 as in 2017 (Figure 1).

Figure 1. Spawner-recruit relationship for fall-run in-river estimates of run size. Number indicates spawner estimate for that year (y-axis) as derived from spawners three years earlier (x-axis). Color indicates winter-spring rearing andmigration conditions for that brood (winter-spring 2015 for spawners in 2017). Red denotes dry year in first winter-spring. Green denotes normal years. Blue denotes wet years. Source: http://calsport.org/fisheriesblog/?p=2205 ).

Reclamation is misleading on raising Shasta

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A September 2018 Bureau of Reclamation “fact sheet” on raising Shasta Dam is misleading.

Enlarging the reservoir will provide an additional 630,000 acre-feet of stored water for the environment and for water users.

Comment: Additional storage would have been accomplished in only two years of the last decade (Figure 1). There would have been no additional cold-water pool volume in critical years 2013-2015, when the loss of cold water was a problem (Figure 2). Water users already had 100% allocations in the years in which raising Shasta would have added storage. Water allocations would likely increase in some dry years following wet years, offsetting any prospective environmental benefit by drawing down storage.

Enlarging the reservoir will improve water supply reliability for agricultural, municipal and industrial, and environmental uses; reduce flood damage; and improve water temperatures and water quality in the Sacramento River below the dam for anadromous fish survival.

Comment: there would have been no flood benefits in the past decade. Critical-year water temperatures from 2013-2015 would not have changed. Sacramento River water quality suffers the most in critical drought years. This would not benefit from raising Shasta.

Figure 1. Daily average flows from Keswick Reservoir over past decade. Raised Shasta would only accommodate added storage in wet year spill events in water years 2011 and 2017.

Figure 2. Shasta storage volume over past decade. Maximum existing storage is 4,552,000 AF.