Category Archives: Water Quality

Low Spring Flows Reduce Survival of Spring-Run Salmon – Lessons 14 and 15

Posted on by

Following an introductory post, this is the fifth post in a series on the lessons learned by the National Marine Fisheries Service (NMFS) from the 2013-2015 drought that devastated Sacramento River salmon populations.  This post addresses NMFS’s Lessons #14 and #15.

NMFS acknowledges that low spring flows may lead to low survival of juvenile spring-run Chinook salmon during their emigration to the sea.  NMFS also suggests that disease may also cause poor survival in dry years.

Some additional observations regarding outmigration are appropriate.  Most wild spring-run fry, fingerling, and pre-smolts emigrate in winter, although spring smolt emigration also occurs.  Another thing to consider is that while disease may be more prevalent in spring of dry years, it may be due to extended rearing in the poor habitat of the upper river in drier years (less food, warmer water, and more stress).  Increased predation by striped bass and other predators under these same habitat conditions is almost certainly another factor.  Lower flows make predators more effective because of lower turbidities, warmer and shallower water, less cover, and slower transport rates.

NMFS’s Lessons 14 and 15 did not consider lower survival of adult salmon migrating upstream in spring of drier, low flow, warmer water years.  However, this is also important.  Run counts are strongly related to water-year types, with poor runs in drier years (Figure 1).  Adults that migrate upstream in spring and over-summer in dry years face more difficult passage in spring and warmer spring and summer water temperatures.  Warmer water temperatures lead to greater stress, energy loss, and disease, poorer pre-spawn survival, and reduced reproductive success (Richter and Kolmes 2005).

An overall lesson is that low winter-spring flows lead to higher water temperatures in the lower Sacramento River migration corridor (Figures 2 and 3) and in spawning tributaries (Figure 4), which in turn reduce survival and reproductive success of spring-run salmon.

A related issue at play relates to Lesson 8 (low flows in the lower Sacramento River at the Wilkins Slough gage).  Low spring and summer flows in the lower mainstem Sacramento River flows lead to warmer spring and summer water temperatures.  This in turn leads to higher predation rates on juvenile salmon and poorer adult survival and reproduction success.  Continuing to ignore long-ago established water quality standards for water temperature and operating norms for flow is putting greater stress on all the salmon runs and on sturgeon.  Spring-run salmon are especially vulnerable because both juveniles and adults are present in the lower Sacramento River in spring.

One especially damaging case occurred in early spring 2018.  A series of storms raised flows in the lower Sacramento River by approximately 50,000 cfs, while at the same time there was only a minimum release of about 3000 cfs into the upper Sacramento River from Shasta Dam.  Substantial flows entered the lower Sacramento River from tributaries and from the outfalls of agricultural basins, including the Butte Basin at the Butte Slough Outfall gates.  Some flow even left the river via overflow weirs into the Sutter Bypass. The sudden surge of urban and agricultural basin stormwater, with high oxygen demand, sediment, and chemical loads, led to a series of fish kills of adult spring-run salmon in the lower Sacramento River at the Butte Slough Outfall (Figures 5 and 6).  It is not clear exactly why high concentrations of stormwater may have increased mortality of spring-run salmon in 2018.  What is clear is that low Shasta releases contribute to higher concentrations of stormwater in river flows at key times during their migration.

In conclusion, Reclamation should consider higher spring releases from Shasta in drier years like 2021 to (1) improve juvenile spring-run emigration survival to the Bay-Delta, and (2) improve adult spring-run survival and reproductive success.  Reclamation should also consider spring pulse flow releases from Shasta-Keswick to emulate natural unimpaired lower river spring flows and to enhance migration success.  Such pulses should be timed with lower river tributary flow pulses.  Finally, as discussed in previous posts, Reclamation’s contractors and others must reduce dry-year water diversions in spring from the mainstem Sacramento and its tributaries to further protect spring-run salmon.

Figure 1. Relationship between Mill and Deer Creek spring run salmon counts 1963-2019. Blue dots represent above-normal and wet years. Yellow dots represent below-normal and dry years. Red dots represent critical dry years. Red margin on blue dots represents a wet and above normal year for adult immigration with a critical dry year two years prior during rearing and emigration. Of special note are the sharply higher run sizes in wet years in Deer Creek, but lower run sizes in Deer Creek in drier years. This shows that production of salmon in Deer Creek suffers proportionally more than in Mill Creek in drier years. In both creeks, salmon runs suffer in years when they are emigrating and immigrating in dry conditions.

Figure 2. River flows (1000s of cfs) in the lower Sacramento River at Wilkins Slough (below the mouths of Deer and Mill Creeks) in winter-spring from 1995-2021. Note very wet conditions in 2006 and very dry conditions in 2014 and 2015.

Figure 3. Water temperatures in the lower Sacramento River at Wilkins Slough (below the mouths of Deer and Mill Creeks) in winter-spring from 2013-2021 (only data available). Note the extraordinarily warm water (near or above 70ºF) in early spring of drier 2014, 2015, 2018, and 2020. State standard is 68ºF. Migrating adult salmon suffer stress and mortality at water temperatures above 60ºF.

Figure 4. River flow and water temperature in Deer Creek 2011-2921. Wet year spring in 2011, 2017 and 2019 shown in blue highlight: other spring conditions shown in yellow highlight. Dry years include 2013-2015 and 2021. The remainder are normal or average year types. Note lower water temperatures in wetter years, with highly stressful temperatures (>68ºF, 20ºC) delayed further into spring than during drier years.

Figure 5. Dead adult spring-run salmon floating at the mouth of Butte Slough Outfall in the Sacramento River in March 2018. Fish likely died from severe stress from low oxygen and heavy suspended sediment and chemical load after being attracted to stormwater flow from outfall gates.

Figure 6. Dead adult spring-run salmon floating at the mouth of Butte Slough Outfall in the Sacramento River in March 2018. Fish likely died from severe stress from low oxygen and heavy suspended sediment and chemical load after being attracted to stormwater flow from outfall gates.
Source: https://youtu.be/t5oB_hWcrzU

Use of Shasta Dam TCD side gates – Lesson #3

Posted on by

Following an introductory post, this is the fourth post in a series on the lessons learned by the National Marine Fisheries Service (NMFS) from the 2013-2015 drought that devastated Sacramento River salmon populations.  This post addresses Lesson #3.

The side gates at the bottom of the Temperature Control Device (TCD) on the inside face of Shasta Dam (Figure 1) allow deeper, colder water in the reservoir to be drawn into the power plant intake penstocks and released to the river below. Use of the side gates allows more colder water to be released for salmon in the river below in summer and fall in years when reservoir levels are low and the cold-water-pool is limited.

In 2014 and 2015, NMFS and the Bureau of Reclamation learned that when the reservoir level is low and the side gates are opened to access cold water, some warmer surface water is also drawn downward into the side gate openings.1 The entrance of some warm water through the side gates compromises temperatures downstream of the dam, thus reducing the effectiveness of the TCD system. Warmer-than-expected release temperatures also limit the ability of Reclamation to meet water demands for downstream contractors when reservoir levels are low. Delaying side gate use with the present structure requires maintaining higher summer storage levels with less summer deliveries.

A comparison of Shasta conditions in mid-August 2014 and mid-August 2015 provides a good example of the problems (Figures 2 and 3). Reclamation used the side gates in August 2014 but not in August 2015. In 2014, Reclamation released more irrigation water in summer, in anticipation of being able to use the side gates (Figure 4). In 2015, lower summer releases conserved storage and cold-water-pool volume, thus delaying use of the side gates. The 2014 operations led to the complete loss of access to the cold-water-pool by October (Figure 5). Water temperatures in 2015 were still too high, but complete loss of control did not occur.

There are other operational changes that may help. Most of the water discharged from the TCD passes through penstocks to powerhouses near the base of Shasta Dam. Those powerhouses are operated based on power demand and prices, not based on temperature management (lower graph of Figure 6). As power demand and power values increase, Reclamation “peaks” the powerhouses to follow these increases. However, the amount of water going through the powerhouses seems to affect the layer of water in Shasta Reservoir that the TCD draws from. and thus the temperature of the dam release water (Figure 6). Low intake rates during non-peak times appear to draw a greater proportion of warmer surface waters from Shasta Reservoir.

It is likely that a more constant rate of release from Shasta Reservoir, rather than peaking, would maintain an overall lower temperature of water that leaves Shasta Reservoir and enters Keswick Reservoir immediately downstream of Shasta. It is also likely that a constant flow of water through Keswick would allow less mixing of Keswick’s warmer surface water with the cooler release from Shasta. This is because water from Shasta would spend less time in Keswick and because a constant release from Shasta would help the cooler water maintain an “underflow” of cooler water at the bottom of Keswick.

Similarly, operation of the powerhouses at Trinity Reservoir and Whiskeytown Reservoir affect the water temperature of water exported from the Trinity River to the Sacramento River system. Most of the water exported from the Trinity to the Sacramento passes through Spring Creek Powerhouse, located on the west side of Keswick Reservoir. All of these powerhouses, too, are operated for power first, not for water temperature. Reduced peaking at these facilities, or simply optimization for water temperature, would help improve water temperatures in the Sacramento River downstream of Keswick Reservoir.

In summary, higher storage levels and greater cold-water-pool volume, delayed use of side gates, changing side gate openings, fixing leaks, and possible changes to peaking power operations may be necessary to protect salmon in the Sacramento River below Shasta Dam.

Figure 1. Shasta Dam Temperature Control Device configuration. Source: Reclamation

Figure 2. Shasta reservoir water temperature profile and TCD operation in August 2014. Note side gate use (curved arrows).

Figure 3. Shasta reservoir water temperature profile and TCD operation in August 2015. Note water level and cold water pool elevations were slightly higher in 2015 than 2014 (Figure 2).

Figure 4. Water temperature and volume of releases to the lower Sacramento River Aug-Oct 2014 and 2015. Note loss of Shasta cold-water-pool access in September 2014. The higher storage releases in August in 2014 compared to 2015 made up much of the storage level differences between 2014 and 2015 shown in figures 2 and 3.

Figure 5. Water temperature profile in Shasta Reservoir and outlet tower Temperature Control Device configuration in October 2014.


Figure 6. Hourly water temperature and release rate from Shasta Dam 10/7-10/12 2014. Note highest water temperatures were during lower non-peaking-power release periods. See Figure 5 for reservoir water temperature profile and TCD operation on 10/8/2014.

  1. TCD leaks at higher elevations were also detected. ↩

Drastic Measure to Meet Delta Outflow

Posted on by

For seven days in mid-March 2021, the Bureau of Reclamation substantially increased Folsom Lake storage releases. Roughly, the releases tripled in volume (Figure 1). The release of over 20,000 acre-feet of water is significant for a year in which Folsom storage is not much better than it was in the worst year on record – 1977 (Figure 2).1 With the release in mid-March, the lake level dropped 3 feet. Yes, there was rain in the forecast and a decent snowpack, but certainly no flood concerns. So why? The reason was to meet state water quality requirements for Delta outflow. Delta outflow increased from 7,000 cfs to 12,000 cfs for a few days (Figure 3).

The outflow pulse was needed to meet an obscure and complicated provision in the Bay-Delta’s D-1641 Water Quality Control Plan called “footnote 11.” The footnote (Figure 4) specifies a formula for determining minimum daily Delta outflow for February through June in different water year types. The base requirement is 7100 cfs 3-day running average minimum (that was being met – Figure 3). What was not met is the requirement in Table 4 to increase Delta outflow from Feb-Jun for the general ecological benefit from higher natural Delta outflow. That requirement is met by meeting a specified average number of days of obtaining an electrical conductivity level (EC) of 2640. Since even that requirement was not met either (Figure 5), the Executive Director of the State Water Board allowed Reclamation and the Department of Water Resources not to meet it.

The primary problem with this Delta Outflow requirement is the abrupt and arbitrary way it is met. If all that is needed to relax the requirement is a “BOGSAT,”2 then all stakeholders need to be involved. Why did Reclamation place the burden primarily on Folsom Reservoir? Why did Reclamation release all the water over just a few days? The abrupt releases likely affected steelhead spawning. The lost storage will likely make salmon migration and spawning in the fall worse as well. At a minimum, Reclamation should have provided some form of notice of this major action. Reclamation should also document the effects.

Figure1. Streamflow in the lower American River at Fair Oaks gage March 8-18, 2021

Figure 2. Storage level in Folsom Reservoir in 2021. Source: CDEC.

Figure 3. Delta outflow in Feb-Mar 2021. Source: CDEC.

Figure 4.  FOOTNOTE 11 in D-1641:  Bay-Delta Water Quality Control Plan

Figure 5. EC at Chipps Island Station D10 in winter 2021.

Figure 6. Daily average Oroville reservoir release in winter 2021.

  1. Lake Oroville provided something less than 10,000 acre-ft, while Shasta Lake provided none. ↩
  2. BUNCH OF GUYS SITTING AROUND a TABLE ↩

Summer Reservoir Releases – Lessons Learned #2

Posted on by

Following an introductory post, this is the third post in a series on the lessons learned by the National Marine Fisheries Service (NMFS) from the 2013-2015 drought that devastated Sacramento River salmon populations.  This post addresses Lesson #2.

In 2014 and nearly again in 2015, Reclamation ran out of cold water in Lake Shasta available for release to maintain downstream salmon in late summer and early fall (Figure 1).  Cutting late spring and early summer water deliveries to contractors from reservoir releases in most cases would preserve cold-water pool through to fall.  In critical drought years 2014 and 2015, cold-water-pool volume on June 1 was about 1.2 million acre-ft.  In wetter 2016 and 2019 cold-water-pool volume on June 1 was more than double that.

In late summer 2014, the available cold-water-pool ran out.  Lower gates of the reservoir outlet tower began taking warmer surface water (Figures 2 and 3).  Even the lowest “river outlets” water was over 60oF by early October.  Water releases in June and July 2014 were near 10,000 cfs (Figure 4).  That level of release was already being capped from the wet year level of 15,000 cfs.  Dropping to 8,000 cfs could have saved another 4,000 acre-ft per day, or about 240,000 acre-ft, which may have sustained cold water releases through early October.

In June-July 2015, releases were dropped to near 7,000 cfs (Figure 4), but even then, water temperature in release water had to be compromised (Figure 5) to sustain some cold water into the fall (Figure 6).  Subsequently, research indicated that the 2015 water temperature limit of 56oF for release water proved insufficient, and that a 53oF limit was necessary to protect eggs and embryo of salmon.  Water temperatures were sustained near or below 53oF from 2016 to 2020 (Figure 6) by limiting June-July releases (see Figure 4).

In summary, capping releases in June-July, in combination with selectively drawing release water from reservoir water layers, was the normal procedure in preserving cold-water-pool release capability through the summer.  However, despite highly restricted releases in critical drought years 2014 and 2015, the cold water ran out and salmon reproduction severely suffered.  The lessons learned were that Reclamation’s temperature target for release water was too high, and that Reclamation’s predictive ability for preserving cold-water releases through the summer was ineffective and could not be trusted.

Figure 1. Cold-water pool volume in Shasta Reservoir in 2014, 2015, 2016, 2019, and 2021 with 1998-2020 average. Source: https://www.usbr.gov/mp/cvo/.

Figure 2. Water temperature profile in Shasta Reservoir and outlet tower Temperature Control Device configuration in August 2014.

Figure 3. Water temperature profile in Shasta Reservoir and outlet tower Temperature Control Device configuration in October 2014.

Figure 4. Shasta/Keswick reservoir water release rate in June-July 2012-2020.

Figure 5. Water temperature profile in Shasta Reservoir and outlet tower Temperature Control Device configuration in August 2015. Note some water was being released from middle gates to preserve cold water pool supply.

Figure 6. Water temperature below Keswick Dam Aug-Nov 2014-2020. Note higher water temperatures in 2014 and 2015.

 

Sacramento River Fall Run Chinook Salmon – 2020 Update

Posted on by

When I last updated the status of the mainstem Sacramento River fall-run salmon below Shasta in a July 2019 post, I expected 2019 in-river escapement to improve from the 2017 record low run (Figure 1). The record low 2017 run had been the consequence of extreme drought conditions during 2015, the third year of a major drought. In contrast, the 2019 run was largely the progeny of water year 2017, a wet year with good spawning, rearing, and migrating conditions for the 2016 salmon brood year. A potential negative ingredient to the 2019 escapement was the poor number of spawners returning in the fall of 2016 that spawned brood year 2016 (Figure 2). Likewise, 2020 escapement ingredients included the record low number of spawners in 2017, as well as poor rearing and migrating conditions in winter-spring of below-normal water year 2018.

In an April 2017 post, I presented the status of the overall fall-run salmon for the Sacramento River basin that included escapement to the mainstem, tributaries, and hatcheries. Updates of those numbers are shown in Figure 3. The total river escapement, like the upper Sacramento in-river escapement, was depressed from 2015 through 2018. Escapement in 2019 improved, but it declined again in 2020. The 2019 and 2020 Sacramento salmon runs were improved over the 2015-2018 drought-influenced runs, but were lower that returns from other wetter years, because their parental spawner numbers were depressed in 2016 and 2017 (Figure 4). Note in Figure 4 the 2019 run is shown by blue-17 to represent the wet year rearing and emigrating conditions for the 2019 run. The figure depicts the positive spawner-recruit relationship and the strong water-year type influence from two years earlier on the adult escapement (run size).

The prognosis for the 2021 and future runs is poor because of the low number of spawners in recent years and drier water year winter conditions in 2018, 2020, and 2021. Restrictions on the 2021 fishery are likely1 despite wet year 2019 conditions. Hopefully, the 2021 run will show improvement with the restricted fishery and better production from wet year 2019.

Figure 1. Fall-run Chinook salmon escapement (run size) in the mainstem in-river Sacramento River 1978-2019. Source: https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=84381

Figure 2. Spawner-Recruit relationship for upper Sacramento River mainstem fall run Chinook salmon. Number is recruitment year (escapement). Spawners are recruits from three years prior. Numbers are log minus 3 transformed. Red is for dry water year two years prior during rearing and emigration. Blue is for wet year. Green is for normal water year. For example: red 17 represents 2017 run that reared in drought year 2015, with spawners (parents) being 2014 run green number.

Figure 4. Sacramento River spawners versus recruits three years later from escapement estimates (Log10X – 4 transformed). Note that some variability likely occurs from a low number of 2- and 4-year-old spawners in the escapement estimates. Numbers are sum of hatchery, mainstem, and tributary estimates from CDFW GrandTab database. Number shown is rearing year (winter-spring) following fall spawning year. For example: “88” represents rearing year for 1987 spawning or brood year. These fish returned to spawn (recruits) in 1990. The red “07” represents the record low run in fall 2009. Red years are critical or dry water years. Blue years are wet water years. Green years are normal water years. Red circles represent adult return years being drier water years. Blue circles represent return years being wet water years. Green circles represent return years being normal water years. Orange square denotes outlier years influenced poor ocean conditions, floods, or hatchery management factors. Note that runs from wet years are up to ten times higher (1 log number) than the drought influenced years, particularly 87-90, 07-08, and 12-15.