Category Archives: Bay-Delta

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.

July-Aug 2020 Delta Outflow – New State Standard Needed

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The State’s Delta outflow standard for July and August varies from 3000 to 8000 cfs on a 14-day average. The standard in in the drier years is 3000 cfs. The standard in wetter years is 8000 cfs in July and 4000 cfs in August.

These standards have been met for the most part over the past five years (Figure 1). Outflow was greater in 2017 and 2019 than these numeric outflow standards since the State also had to meet the Delta salinity standard that in wet years extends into August. The outflow standard in August 2015 (3000 cfs) was not met under a State Board emergency order in the third year of drought.

The July and August Delta outflow standard should be a 10,000 cfs minimum daily average tidal flow at Rio Vista in the Sacramento River (Figure 2) and 2000 cfs minimum daily average tidal flow at Jersey Point in the San Joaquin River (Figure 3). In addition, a standard of -2000 cfs in False River (Figure 4) is needed to protect endangered smelt and salmon, as well as to protect water quality in the central Delta.1

Standards should also be set to protect against extreme events and circumstances. An example is salt intrusion and high water temperatures in the Delta, such as occurred in a heat wave in mid-August 2020 (Figure 5 and 6). Water temperatures of 23-25oC in the low salinity zone (500-6000 micro-mhos conductivity) are rare and highly detrimental if not lethal to smelt and salmon. Delta exports were raised from 6,000 cfs to 10,000 cfs from 8/10 to 8/22. Delta inflows were raised 4000 cfs during the period to accommodate increased exports (Figure 7). The increasing inflows helped bring warm water from the interior Central Valley into the Delta (Figure 8).

Such conditions should be avoided at all costs. This can be achieved by limiting exports, reservoir releases, or both. August is a peak month of the fall-run salmon migration into the Sacramento Valley. Such high water temperatures would be lethal or avoided with the run being delayed and salmon holding in the Bay. The Delta smelt population concentrates primarily in the low salinity zone, and water temperatures higher than 25oC are lethal to Delta smelt.

I acknowledge the difficulty in meeting these proposed standards, especially in drier years, but they must be adopted to protect the salmon and smelt. New standards are essential for the Delta’s recovery.

Figure 1. Delta outflow in summer of years 2015-2020. Note difference in August between wet (2017, 2019) and drier (2015, 2016, 2018, 2020) years.

Figure 2. Daily average (tidally filtered) flow in the Sacramento River channel at Rio Vista in the north Delta in summer 2020 and average of last 22 years.

Figure 3. Daily average (tidally filtered) flow in the San Joaquin River channel at Jersey Point in the west Delta in summer 2020 and average of last 22 years.

Figure 4. Daily average (tidally filtered) flow in the False River channel in the west Delta in summer 2020 and average of last 22 years.

Figure 5. Water temperature and salinity (specific conductance) at Jersey Pt in the San Joaquin channel of the west Delta in summer 2020.

Figure 6. Water temperature and salinity (specific conductance) at Decker Is in the Sacramento River channel of the west Delta in summer 2020.

Figure 7. Daily average flow in the Sacramento Rivers channel in the north Delta near Freeport in July-August 2020. Note the flow pulse in late August from reservoir releases to meet Delta export increase.

Figure 8. Hourly water temperature of the Sacramento River at Rio Vista in July-August 2020.

  1. A tide gate on False River would help accomplish this objective. ↩

Franks Tract Futures Project

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The Franks Tract Futures Project is asking for additional comments on the State’s revised concept design.1 The project is an outgrowth of the State’s 2016 Delta Smelt Resilience Strategy, which recognized that Franks Tract is a death trap for state and federally listed Delta smelt.

The original design for the project included tide gates to keep salt and smelt from moving upstream from the western Delta into Franks Tract via the False River channel. Once in Franks Tract, the smelt would most assuredly not survive. A new design “transforms the project from an early focus on establishing habitat for the endangered Delta smelt to a project that has sought input from a broad range of stakeholders.” According to the project leader, Brett Milligan from University of California:

Balancing the project’s goals has been a challenge. The first round of this project, the feasibility study, met the water quality and ecology requirements but did not meet the recreational and local economy (requirements). We heard you loud and clear. More or less, this entire last year has been to try to bring in that third tier and to balance these and see if there’s a way that the project can meet all of these criteria and be beneficial to all. The original project design failed to earn public support after it was presented in January 2018. At a crossroads, the project managers made a critical decision. They scrapped the proposal and formed an advisory committee of stakeholders with varied interests in Franks Tract rather than try to force the initiative through the process, while fighting the public every step of the way.

The new design drops the barrier/gate option as “a non-starter,” Brett explained to me. But that was the essential element of the project – stopping salt (and smelt) intrusion into the interior Delta due to the pull of the south Delta export pumps. A temporary barrier has been installed in False River in drought years to protect Delta water supplies.

The conflict is over recreational access to Franks Tract from the west via False River. A similar barrier on Montezuma Slough further west in Suisun Marsh resolved a similar conflict with a boat passage lock that maintains boating access when the barrier is in use.

At this phase of design and permitting, it would seem wise to evaluate an alternative with the barrier that includes a similar boat passage facility, so that the affected public can understand the tradeoffs. That is the purpose of the environmental review process.

June 2020 Delta Outflow – New State Standard Needed

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I recommended a new June Delta outflow standard of 10,000 cfs in a post on June 23 2020. This increase from the current standard of 7000 cfs would keep salt and Delta smelt out of the Central Delta and better maintain adequate water temperatures for emigrating Central Valley salmon smolts.

In this post, I consider the recommended 10,000 cfs value in the context of how the California Department of Water Resources (DWR) and the Bureau of Reclamation (Reclamation) estimate Delta outflow as they manage Delta hydrology and federal and state exports from the south Delta. This should further explain why an increase in the June Delta outflow standard is necessary.

It helps to recall my description in a September 2019 post how DWR and Reclamation estimate Delta outflow: “Delta Total Outflow is a daily-average algorithm calculated in cubic feet per second (cfs) for Station DTO, a hypothetical location near Chipps Island in Suisun Bay.“ This is different from the US Geological Service’s (USGS) method of calculating real-time outflow. As an example, I overlaid the DWR and USGS for the summer of 2018 (Figure 1).

The State’s D-1641 June water quality standard is: the monthly average of the average outflow for each day must meet or exceed 7000 cfs (monthly average of daily averages). DWR and Reclamation comply with this standard using their own estimation method, not real-time outflow. Figures 2 and 3 below show the differences in the DWR and USGS methods in May-June 2020.

In May-June 2020, DWR and Reclamation maintained Delta outflow (using their own estimation method) near 7000 cfs, except during a mid-May storm when estimated outflow reached a peak of 15,300 cfs (Figure 2). But viewed from a different perspective, there were significant dips in the USGS estimation of outflow during spring tides around June 5 and June 19. The DWR method of estimating didn’t pick up these dips at all. These periods where USGS showed negative net outflow showed up in the monitoring of salinity as well (Figures 4-6). Periods of low or negative outflow were also periods of high salinity at key Delta monitoring stations.

Although net daily Delta flows are relatively small compared to real-time tidal flows (Figures 7 and 8), net flows affect water quality and fish habitat conditions on a daily basis. The salinity data for May-June 2020 at False River (Figure 5) is particularly significant. (Note the spikes in salinity during spring tides around June 5 and June 19). False River is the gateway to Franks Tract. As salinity increases in False River, smelt will move upstream (towards lower salinity conditions) in Franks Tract. As I described in an April 28, 2020 post, Franks Tract is a “smelt trap” where smelt that enter almost invariably perish.

Increasing the standard for June Delta outflow so that the required monthly average of the average outflow for each day is 10,000 cfs, not 7,000 cfs, would not fully offset the effects of spring tides and the use of averaging in DWR’s method of calculating compliance. But it would help protect Delta habitat from salt intrusions during spring tides and keep the low salinity zone and young Delta smelt out of the Delta. Although DWR and Reclamation did a good job in May-June 2020 of staying above 7000 cfs each day using their calculated outflow method, adding an explicit minimum daily flow standard to the monthly flow standard could also help. This would likely have the result of reducing exports during periods of the spring tides in the monthly lunar tidal cycle.

Figure 1: Daily outflow estimated by DWR and USGS in summer 2018.

Figure 2. DWR’s calculated Delta outflow in May-June 2020. Note switch to July standard of 5000 cfs

Figure 2. DWR’s calculated Delta outflow in May-June 2020. Note switch to July standard of 5000 cfs outflow on July 1. Source: CDEC.

Figure 3. USGS’s estimate of tidally filtered Delta outflow as estimated in May-June 2020. Spring-tides occurred May 9, May 23 (not measured because of storm inflows), and also on June 5 and June 19. Note dips in outflow on June 5 and 19; these dips do not appear in DWR’s estimate in Figure 2.

Figure 4. Salinity (conductivity) in eastern Suisun Bay at Collinsville in May-June 2020. Note peaks in salinity during net negative outflow with spring tides on June 5 and 19 (see Figure 3).

Figure 5. Salinity (conductivity) in False River in west Delta in May-June 2020. Note peaks in salinity during net negative outflow with spring tides on June 5 and 19 (see Figure 3).

Figure 6. Salinity (conductivity) in eastern Suisun Bay at Pittsburg in May-June 2020. Note peaks in salinity during net negative outflow with spring tides on June 5 and 19 (see Figure 3).

Figure 7. Hourly river flow and tidally filtered flow in lower San Joaquin River channel in western Delta at Jersey Point in June 2020. Note highly negative peak flows with spring tides on June 5 and June 19.

Figure 8. Hourly river flow and tidally filtered flow in lower Sacramento River channel in western Delta at Rio Vista in June 2020. Note spring tides on June 5 and June 19.

Delta Smelt Sanctuary – Deepwater Ship Channel

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In a March 2020 post, I described where the remnants of the endangered Delta smelt population spawn and rear in the Sacramento Deepwater Ship Channel (Ship Channel) in the north Delta (Figure 1). In this post, I describe how the rearing conditions in the Ship Channel are poor. This can be seen by comparing habitat conditions in the Ship Channel with those in the lower Sacramento River channel at Freeport several miles to the east in late spring 2020.

Net Flow

Net flow (cfs) in the Ship Channel remains near zero, since the gate at the north end of the channel near Sacramento remains stuck in the closed position as it has been for several decades (Figure 2).

Water Temperature

Water temperature (oC) is significantly higher in the stagnant flows of the Ship Channel than at Freeport, often reaching into the lethal range 23-25°C for Delta smelt (Figure 3).

Salinity

Salinity (conductivity) is much higher in the Ship Channel because of discharges from urban sewage treatment plants and agricultural operations (Figure 4).

Turbidity

Turbidity is much higher in the Ship Channel due to higher plankton production and port-bound ship traffic in the relatively shallow and narrow Ship Channel (Figure 5).

Dissolved Oxygen

Dissolved oxygen levels are much lower in the Ship Channel because of warmer water, high concentrations of suspended organic sediments, and higher plankton production (Figure 6).

Interpretations and Conclusions

Delta smelt are attracted to the Sacramento Deepwater Ship Channel in winter and early spring to spawn in the relatively warm, low salinity, turbid, and more productive water. The adult smelt can also easily tidal-surf up the ship channel without having to content with strong downstream currents of the Sacramento River channel. Their eggs hatch early to an awaiting abundant plankton food supply. However, in spring the Ship Channel lacks net downstream flows to carry the young smelt to the Bay. By late spring, water temperatures in the Ship Channel reach lethal levels for the young smelt.

Opening the gate at the north end of the Ship Channel would help to alleviate the problems by providing net flow with cooler water temperatures, and by flushing and diluting the stagnant waste waters in the Ship Channel. An operable gate at the head of the Ship Channel would allow adaptive management of the habitat conditions for smelt.

Figure 1. Locations where Delta smelt young were captured in EDSM surveys in July 2019. Circles represent regions. Numbers are total July catch in region. The 94 represents the young smelt captured in the Deepwater Ship Channel.

Figure 2. Net daily flow (cfs) in the Ship Channel and in the Sacramento River at Freeport in June 2020. The green line shows flow in the Ship Channel.

Figure 3. Water temperature in the Ship Channel and Sacramento River at Freeport in June 2020. The blue/purple line shows the water temperature in the Ship Channel.

Figure 4. Conductivity (salinity) in the Ship Channel and Sacramento River at Freeport in June 2020. The green line shows salinity in the Ship Channel.

Figure 5. Turbidity in the Ship Channel and Sacramento River at Freeport in June 2020. The blue/purple line shows turbidity in the Ship Channel.

Figure 6. Dissolved oxygen in the Ship Channel and Sacramento River at Freeport in June 2020. The green line shows dissolved oxygen in the Ship Channel.