Category Archives: Water Quality

Tuolumne River Salmon Runs in Decline – End-of-Year 2020 Status

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After decades of dominating the overall salmon run in the San Joaquin River watershed, the salmon run in the Tuolumne River now lags behind the runs in her sister rivers.  The Tuolumne River is a San Joaquin River tributary with no hatchery.  Its salmon runs are declining (Figure 1).  Unlike her sister rivers the Stanislaus and the Merced, the Tuolumne salmon run did not rebound as well after the 1987-1992, 2007-2009, and 2013-2015 droughts (Figure 2).

The Tuolumne run has had difficulty recovering from droughts because spawner numbers in subsequent years are too low.  There is a positive spawner-recruit relationship, heavily influenced by water year conditions (Figure 3).  Recruitment (run size) is influenced by the number of parent spawners (three years earlier), poor rearing year conditions (two years earlier), and poor conditions in the year adults return.. Runs from 1990-1992 had all three of these adverse conditions, which led to a 99% loss of their potential (two log levels).  The third years of the two recent droughts (2009 and 2015) had similar reduced potential, though with only two of the adverse conditions (poor rearing conditions and poor adult returns).

In a recent post, I related near-record-low salmon runs over the past several years in the Yuba River, a Sacramento River tributary that is similar to the Tuolumne in that it has no hatchery.  Like the Yuba, the Tuolumne salmon run is also markedly influenced by hatchery strays from other Central Valley rivers.  Hatchery strays from other rivers (Figure 4) dominate otherwise poor runs in the Tuolumne River in the years following droughts.  Many Battle Creek and Mokelumne River hatchery smolts trucked to the Bay in 2014-15 later strayed to the Tuolumne River to spawn.

Lack of returning wild salmon that are of Tuolumne River origin, and the dominance of hatchery strays after droughts, do not bode well for the native Tuolumne salmon run.  Resource agencies and other science experts have recommended maintaining a run of at least 500 native spawners for the run to remain “viable” (McClain 2010).  While recent runs since the 2013-15 drought have averaged near 1000 spawners, the fact that 60-70% are hatchery strays indicates that this goal has not been met over the past 15 years.  To increase wild salmon production, the State Water Board needs to adjust the allocation of Tuolumne River water, a process the State Water Board began in 2018.  Changes in the operation of the Delta pumps to reduce pumping during the emigration season would improve the success of all San Joaquin watershed salmon runs.  As native populations improve, river managers could reduce the influence of hatchery strays by ‘sorting out’ strays at the adult counting weir in the lower Tuolumne River; however, this would necessitate marking all Central Valley hatchery smolts.

Figure 1. Fall run Chinook escapement to the Tuolumne River 1975-2019. Data Source.

Figure 2. Fall-Run Chinook salmon escapement in San Joaquin River tributaries 1975-2019. Data Source.

Figure 3. Spawner-recruit relationship for Tuolumne River fall-run Chinook salmon. Numbers are log transformed minus 1 (2.00 = 1000). Numbers are recruits in their spawning return year. Red number is dry water year two years earlier when rearing as young. Red circle is dry year adult return year. Blue is wet year. Green is normal water year.

Figure 4. Source of hatchery strays in Tuolumne River spawning ground surveys in 2016 and 2017. Note only 25% of hatchery smolts are marked. Source.

Winter Pulsed Flow for Salmon Needed Now!

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Winter pulse flows benefit fall-run salmon fry by helping them emigrate to the Delta and Bay nursery areas (see discussion in February 2019 post). The tailwater spawning reaches of dams need reservoir releases to stimulate emigration of fry (Figure 1). Such releases piggy-back on stormwater flows in downstream tributaries, such as those in late January 2021 (Figure 2).

Nearly all Central Valley reservoirs are capturing recent high precipitation from their upper watersheds. With forecasts of further substantial rainfall into mid-February 2021, modest reservoir releases would provide substantial potential benefits to Central Valley salmon populations.

Figure 1. Sacramento River fall-run salmon fry catch near Red Bluff (river-mile 240) in winter 2020. Note that flow pulses stimulated winter fry emigration.

Figure 2. Flows from Shasta/Keswick reservoirs (river-mile 300, brown) and at downstream sites Bend Bridge (river-mile 250, green) and Wilkins Slough (river-mile 125, blue) in winter 2021. Note that tributary inflows created flow pulses in lower reaches of the Sacramento River.

Longfin Smelt – 2020

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In a February 2020 post on the status of longfin smelt, I lamented the poor 2019 population index (Figure 1) and thus made a grim prediction for the future of the Bay-Delta sub-population of this state-listed endangered species.  The index in wet year 2019 should have been 10 times higher (one higher in log number).  Preliminary survey results suggest that the 2020 population index for longfin smelt will likely be as poor as those in 2018 and 2019.

In Figure 1 below, the 2020 index will likely show as a red 20 just above the red 14.  Most of the 2020 spawners came from the 2018 spawners (green 18 in Figure 1).  Like the 2018 spawn, the 2020 year class grew up in a drier year, upstream in Suisun Bay and the western Delta (Figure 2), as compared to a more western Bay distribution like wet year 2019 (Figure 3).

I am very concerned what will happen if winter 2021 stays dry and there are thus two dry water years in a row (2020 and 2021).  This would drive the 2021 production index down to 2015-16 levels.  Coupled with the absence of Fall-X2 flows in 2020 and the unusually low 2019 longfin index, a second straight dry year presents a serious threat to the population index in 2021 and future years.

Figure 2. Longfin smelt catch distribution in 2020 Survey 1 of 20-mm Survey. Delta outflow was 8,000-20,000 cfs. Source.

Figure 3. Longfin smelt catch distribution in 2019 Survey 1 of 20-mm Survey. Delta outflow was 160,000-180,000 cfs. Source.

 

Scott River Chinook Salmon Update

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The Scott River Chinook salmon, a key contributor to the overall Klamath River salmon run, are in major trouble.  In a November post, I had a “mixed” prognosis for this year’s fall run.  Well the numbers are now in – a record low, bleak run of 117 spawners observed (Figure 1) at the weir downstream of Fort Jones.

Figure 1. Scott River fall run salmon escapement 1978-2020. Source: CDFW unpublished data.

The poor run can be directly attributed to lack of fall river flow, a fact that I had addressed in a 2017 post.  Salmon simply cannot ascend the lower Scott River into Scott Valley spawning grounds from the Klamath River because of lack of streamflow.  Some may spawn in the steep canyon below the Valley (and counting weir), but poor spawning habitat and low flows in the canyon offer little solace for the salmon.

Poor fall flows (Figure 2) can be directly attributed to fall groundwater extraction and surface water diversions for hay-pasture irrigation.  The State Water Board should stop crop irrigation after October 1.  This irrigation practice has been getting worse over the past several decades, aided by improved well extraction and sprinkler technology and greater demand and higher revenues.  Present water use permits allow irrigation into December, which ranchers have been taking advantage of to get an extra crop of hay (with the help of climate change).

Unlike 2020 (Figure 2), water use in past drought years tapered off earlier and flows increased during October (Figures 3-5).  This allowed fall-run salmon access to the Valley.  In contrast, recent wet and normal years see a combination of precipitation and reduced water use, which enhances fall flows (Figures 6 and 7).

In conclusion, the State Board should limit fall water irrigation in Scott Valley to save the salmon.  The Sustainable Groundwater Management Act (SGMA), passed in September 2014, requires local agencies to develop Groundwater Sustainability Plans (GSP) that will assess and project future groundwater conditions, and provide management and monitoring activities.  The Scott River basin is a priority basin.  Siskiyou County is required to develop and submit a GSP for the Scott River basin by January 31, 2022.  A preliminary plan recently developed by the advisory group suggests reducing irrigation acreage (Figure 8) to increase streamflow (Figure 9).  That would help, but what salmon need is a cutoff of irrigation by October 1.  An option for further augmentation is to employ unused groundwater extraction wells in the fall to add water to the river  for short periods.  Stored water in the tailings ponds (red area in Figure 8) could also be gravity-fed or pumped into the river at critical times.

Figure 2. Scott River flow fall 2020. Water year 2000 was a drought year.

Figure 3. Scott River flow fall 2000 and winter-spring 2001. Water year 2001 was a drought year.

Figure 4. Scott River flow fall 2013 and winter-spring 2014. Water year 2014 was a dry year.

Figure 5. Scott River flow fall 2014 and winter-spring 2015. Water year 2015 was a normal year.

Figure 6. Scott River flow fall 2016 and winter-spring 2017. Water year 2017 was a wet year.

Figure 7. Scott River flow fall 2017 and winter-spring 2018. Water year 2018 was a below normal water year.

Figure 8. Baseline (present) and preliminary action alternative for Scott Valley irrigation. Source: preliminary plan.


Figure 9. Analysis of preliminary action alternative. Source: preliminary plan.

 

 

May-September Delta Water Temperature Standard Needed

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In a 9/22/20 post, I suggested summer Delta outflow standards. In this post I suggest a spring-summer water temperature standard for the Delta as further protection for salmon and smelt. Water temperatures above 23oC (73oF) are harmful to salmon and smelt, which live and migrate through the north and west Delta throughout the summer. Much of the Delta smelt population that remains is located in these regions especially in dry years.1 Spring-run and winter-run salmon migrate upstream through the area in late spring. Fall-run salmon migrate upriver through the summer.

Harm occurs as stress, higher predation, avoidance reactions, poor growth, and reduced long-term survival and reproduction. At higher temperatures (>23oC) migration blockage and mortality occurs. Such temperatures are commonly reached or exceeded in the north Delta even in wetter, water-abundant years.

High water temperatures occur in the Delta when there are high air temperatures and/or low freshwater inflow and outflow. Such conditions are becoming more frequent with climate change. A good example occurred in water year 2020, which featured low precipitation, low snowpack, and high air temperatures.2 Because water managers cannot control air temperatures or watershed precipitation, they must manage Delta inflows from reservoir releases and outflows through the Delta to improve water temperature control in May-September, especially in drier years.

To protect smelt and salmon, there need to be reasonable water temperature standards in the Delta. The existing water temperature standard in the lower Sacramento River above the Delta is 68oF, but managers of the state and federal water projects pay it almost no heed. There is no existing standard for the Delta. The north Delta water quality standard for the Sacramento channel in wet years should be 70oF (21oC) at Freeport and at Rio Vista. In normal and dry water years, the standard should be 72oF (22oC) at Freeport and at Rio Vista. In critical drought years, the State Water Board needs to require additional Delta inflow and curtail exports as needed to respond to extreme events (e.g., water temperatures greater than 75oF during heat waves). At critical times, a change of only a degree or two will help limit fish stress and mortality.

Higher Delta outflow and lower exports are appropriate prescriptions for maintaining reasonable water temperatures in the Delta (see Figures 1-3 and caption notes). For example, in July and August 2020 (Figures 1-3), increased inflow into the 14,000-16,000 cfs range from 12,000 cfs at Freeport could have held water temperature below 22oC. Note in Figure 3 that increased inflow can be captured by south Delta exports (Figure 3). However, during heat waves under extreme drought conditions, the State Board should also limit exports to retain outflows from the Delta to keep the low salinity zone out of the warmer Delta. Otherwise, exports will reduce the portion of Delta inflows (Freeport flows) that reach Rio Vista.

Such standards are achievable, albeit at significant water supply cost. They are worth the effort. High summer water temperatures, such as those that occurred in wet year 2019 and dry year 2020, must be mitigated. The 23-25oC conditions in summer 2020 (portrayed in Figures 1-3) should not occur, and would not under the suggested Delta water temperature standard. For wet years such as 2019 (Figure 4) and 2017 (Figure 5), water temperatures should be kept at or below 70oF (21oC) by maintaining Freeport near 20,000 cfs as needed.

In summary, Delta water quality standards should be adopted for inflow, outflow, and water temperature to protect salmon and smelt in the warmer months of the year, May-September. Such standards are needed because of recent changes in water project operations and the effects of climate change.

Figure 1. Water temperature and salinity in the west Delta near Rio Vista in spring-summer 2020. Note Delta draining in neap-tide periods generally brings warmer water downstream into the west Delta, except in mid-August event when a heat wave drove water temperatures up into 23-25oC range. This event was accentuated by higher exports and associated high Delta inflows.3

Figure 2. Water temperature and net river flow (tidally filtered) in the lower Sacramento River at Freeport in the north Delta in spring-summer of dry year 2020. Note that it took flows at or greater than 16,000 cfs to keep temperatures near 70oF (21oC).

Figure 3. Sacramento River flow at Freeport (FPT), water temperature at Rio Vista (RVB), and south Delta exports at Tracy (TRP) and Banks (HRO) pumping plants in south Delta from May-Oct 2020.

Figure 4. Water temperature and net river flow (tidally filtered) in the lower Sacramento River at Freeport in the north Delta in spring-summer of wet year 2019. Note that it took flows at or greater than 16,000 cfs to keep temperatures near 70oF (21oC).

Figure 5. Sacramento River flow at Freeport (FPT-Y1) and water temperature at Freeport (FPT-Y2) and Rio Vista (RVB-Y2) from May-Oct 2017.