Delta Smelt Resiliency Strategy – Update Fall 2018

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

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

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: ).

Reclamation is misleading on raising Shasta

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.

Lower Sacramento River Water Temperatures A 5-Year Adaptive Management Study of Lower Sacramento Summer Flows and Water Temperatures

Nearly three decades ago, state and federal regulators made prescriptions that required the maintenance of water temperatures in the lower Sacramento River below 68oF (20oC) in summer to protect salmon, sturgeon, steelhead, and water quality. The condition was put in water right permits, anadromous fish restoration plans, and in the state’s water quality plan for the basin. Summer is the season when once-abundant spring, fall, and winter run salmon ran up the river and to tributaries to spawn. It is also the rearing season for spring-spawning sturgeon, striped bass, American shad, splittail, and trout, all once abundant in the lower Sacramento River watershed.

The effect of how the prescription was administered in the early 1990’s can be seen in water temperature record for Wilkins Slough in the lower Sacramento River near Grimes (Figure 1). The gradual erosion in the application of the prescription is also apparent over the past two decades. Lack of enforcement of the prescription by federal and state regulating agencies in the last five years is also apparent even in the recent wetter years following the critical drought years of 2013-2015.

I looked at the last five years, 2014-2018, as an adaptive management study to determine how to maintain the 68oF prescription. Plots of water temperatures and river flow from Wilkins Slough (Figures 2-6) are unequivocal evidence that river flow is the primary driver of summer water temperatures in the lower Sacramento River near Wilkins Slough. Air temperature is a lesser factor in summer because it is nearly always warm. A rise in flow over the summer of 2018 (Figure 6) shows clearly that keeping flows in the 6000-8000 cfs range (depending on air temperature) can maintain water temperature near the 68oF target. Flows in the 3000-5000 cfs range lead to water temperatures of 72oF or higher, which are very detrimental to the dependent fish.

Finally, the gradual decline in summer river flow at Wilkins Slough over the past two decades (Figure 7) matches the rise in summer temperatures (Figure 1). It is not a question of changing water quality standards to protect fish. It is simply a question of enforcing the existing standards and water right permit requirements. Increasing Shasta Reservoir releases, limiting water diversions, or some combination thereof, could provide the necessary flows.

Figure 1. Water temperatures recorded at Wilkins Slough in the lower Sacramento River from 1980 to 2018.

Figure 2. Water temperature and river flow at Wilkins Slough May-August 2014.

Figure 3. Water temperature and river flow at Wilkins Slough May-August 2015.

Figure 4. Water temperature and river flow at Wilkins Slough May-August 2016.

Figure 5. Water temperature and river flow at Wilkins Slough May-August 2017.

Figure 6. Water temperature and river flow at Wilkins Slough May-August 2018.

Figure 7. River flow recorded at Wilkins Slough in the lower Sacramento River from 1980 to 2018.