Author Archives: Tom Cannon

The Delta in April-June 2022 under TUCP

Posted on by

A lot has been said about the drought’s effect on water supplies for cities and farms, but little is said about how Delta fish are faring.  Freshwater inflow to the Delta was about half of normal in April through June 2022 because of the State Water Board Order approving the Department of Water Resources (DWR) and the Bureau of Reclamation’s Temporary Urgency Change Petition  (TUCP) for Delta operations.  With some of this limited Delta inflow going to water users during April, May and June, little was going to the fish.

The State Water Board granted the TUCP because Central Valley reservoir storage was so low at the end of winter in this third year of drought.  During drought, most of the Delta’s late spring and summer inflow comes from releases from storage in Shasta, Oroville, and Folsom reservoirs.

The TUCP has ended, and the normal operating rules for the Delta under Water Rights Decision 1641 have gone back into effect as of July 1.  It is now a good moment to review the effects of this most recent TUCP.

Conditions Under TUCP (April-June 2022)

Delta inflow from the Sacramento River and tributaries averaged about 7500 cfs while the TUCP was in effect (Figure 1).  Releases from Folsom Reservoir averaged 1000-2000 cfs of this inflow.  Releases from Oroville Reservoir varied widely, but averaged about 2500 cfs over the period.  Other inflow came from the Sacramento River (Shasta Reservoir) and its tributaries, which during the TUCP period averaged about 3000-4000 cfs.  The San Joaquin River and its tributaries contributed on average another 1000 cfs to Delta inflow.

There are three main uses of Delta inflow when inflow is low: repelling salt water, south Delta exports, and in-Delta use.  South Delta exports were about 1300 cfs while the TUCP was in effect.  Delta outflow, holding back the salt water, required roughly 4000 or more depending on tides.  Net in-delta use (water diversions other than south Delta exports) accounted for the rest.

Salinity (EC, mS/cm) at Emmaton (west Delta Figure 2) , normally kept near 500 per the state standard for agriculture, increased to levels ranging from 500 to 8000 (Figure 2), with daily average of 2000 to 4000, four to eight times the standard.

At Jersey Point, where the standard is 450-750 EC, salinity ranged from 1200 to 2300 in June (Figure 3).

Conditions After TUCP (Early July 2022)

After the TUCP expired, conditions changed as regulatory requirements returned requirements under Decision 1641.  Delta inflow increased to 12,500 cfs (Figure 1).  At this date, salinity has fallen toward the appropriate salinity standards (Figures 3 and 4).

What does this mean for the Delta and its Fish? 

  1. The agricultural salinity standard of 500 mmhos at Emmaton near Sherman Island in the Sacramento River channel was “relaxed” under the TUCP (Figure 3). Salt water was able to push further upstream and mix to a further extent with inflow.  The daily salinity (EC) range of approximately 500-8500 mmhos, an increased level of spring salinity not seen since the 2014 and 2015 drought under earlier TUCPs.
  2. Likewise, the average daily salinity (EC) standard at Jersey Point near Sherman Island in the San Joaquin River channel (Figure 4) was also not being met.
  3. Salinity was managed under the TUCP to meet the minimum drinking water standards (<800 mmhos) near municipal water supply diversions in the central Delta (Figure 5). (I would not drink this water or put it on plants.)
  4. Throughout June, net flows in the Old and Middle River channels in the central Delta were southward toward the South Delta export pumps (Figures 2 and 6).
  5. While the TUCP was in effect, salt water moved upstream in the Sacramento River channel near Rio Vista and into Cache Slough (Figure 7). Within the Cache Slough Complex, water moved upstream (Figure 8) in part due to water diversions in the north Delta.
  6. Delta inflows from the Sacramento River at Freeport fell below 10,000 cfs from April through June 2022 as allowed under the TUCP (Figure 1). This drop led to the increases in salinity noted in Figures 2-8.
  7. Low Delta inflows also contributed to higher water temperatures throughout the Delta during and after the TUCP period (Figures 9 and 10). Water temperatures above 72 degrees are detrimental to most of the native Delta fish.

Conclusions:

  • The TUCP allowed reduced Delta inflows that preserved some reservoir storage in critical drought year 2022.
  • Inflows dropped below the normal 10,000-12,000 range that keep Delta salinity at Emmaton and Jersey Pt below the 500 mmhos agricultural salinity standard.
  • Central and north Delta water diversions from the Delta’s pool of freshwater contributed to upstream movement and loss in quality and quantity of the low-salinity zone, a critical nursery habitat of Delta native fishes.
  • The shift in the location of these important habitats into the north and central Delta, and the associated warming from the more-eastward position and lower net flows represent a serious impact on Delta native fishes including Delta smelt, longfin smelt, green and white sturgeon, winter-run, fall-run, and spring-run salmon, and steelhead, which use these habitats through the spring and summer for rearing and migration.

Figure 1. Delta inflow (cfs) from the Sacramento River as measured at Freeport in 2022. Note the TUCP allows streamflow at Freeport to be reduced below the 10,000-12,000 cfs range that is normally necessary to meet Delta salinity standards at Emmaton and Jersey Pt.

Figure 2. West Delta salinity gage locations with net flow direction during TUCP period April-June 2022.

Figure 3. Salinity (EC) range at Emmaton in west Delta in 2022.

Figure 4. Salinity (EC) at Jersey Point in west Delta in 2022.

Figure 5. Salinity (EC) in the central Delta in Old River channel in 2022.

Figure 6. Net flows in central Delta Old River and Middle River channels in 2022.

Figure 7. Salinity (EC) in Cache Slough channel of north Delta near Rio Vista in 2022.

Figure 8. Net flows in Cache Slough near Liberty Island in 2022.

Figure 9. Water temperature of the Sacramento River near Freeport in 2022.

Figure 10. Water temperatures in the Delta and Delta inflows May-July 2022.

EMM – Emmaton on the Sacramento River channel in west Delta.

WLK – Lower Sacramento River below Wilkins Slough above the mouth of the Feather River.

PPT – Prisoners Pt in the central Delta channel of the San Joaquin River.

DLC – Sacramento River channel in the north Delta at the Delta Cross Channel.

OBI – Old River in central Delta.

RVB – Rio Vista Bridge in west Delta channel of the Sacramento River.

SJJ – San Joaquin channel in west Delta at Jersey Pt.

OH4 – Old River in central Delta.

ANH – San Joaquin River channel of west Delta at Antioch.

MSD – San Joaquin River channel at entrance to Delta at Mossdale.

Cache Slough Tidal Wetland Restoration – Update More misguided resource-damaging habitat restoration for an already highly altered and compromised Delta

Posted on by

Cache Slough Complex Restoration

The Cache Slough Complex is in the lower (southern) Yolo Bypass in the north Delta region (Figure 1). It is the focus of the state’s tidal wetland restoration EcoRestore Program that spans 16,000 acres in the Cache Slough region of the Sacramento-San Joaquin Delta.

The 53,000-acre Cache Slough Complex is located in the northwest corner of the Sacramento-San Joaquin River Delta in Solano and Yolo counties (Figure 1). The Yolo Bypass receives inflow directly from the Sacramento River (Fremont Weir), the Colusa Basin Drain, Putah and Cache creeks, and agricultural and municipal discharges. The Cache Slough Complex exits the Yolo Bypass via Cache Slough, first connecting to the outlets of Miner and Steamboat Sloughs, before entering the tidal Sacramento River channel near Rio Vista.

The Cache Slough Complex has been identified as an area with great potential for tidal restoration as a result of its connectivity with the Yolo Bypass floodplain, suitable elevations, high turbidity, high primary and secondary productivity, and use by Delta smelt (Hypomesus transpacificus), Chinook salmon (Oncorhynchus tshawytscha), and other native fishes. Both federal and state wildlife agencies consider the Cache Slough Complex to be a prime area to advance habitat conservation to benefit endangered species in the Sacramento-San Joaquin Delta and incorporate improvements to the regional flood management system.

The latest project approved for construction is the Lookout Slough Project, a 3000-acre tidal marsh restoration immediately to the west of Liberty Island. The Project was certified by DWR in 2020 as mitigation/compensation for the Delta Tunnel Project. The Delta Stewardship Council recently denied appeals1 to the state’s certification of the Lookout Slough tidal marsh restoration project. Once completed, Lookout Slough will be the Delta’s largest single tidal habitat restoration project to date.

The Problem

Most of the tidal “restoration projects” in the Cache Slough Complex involve breeching leveed tracts of agricultural land to create subtidal or intertidal habitat. Tidal waters once confined to narrow floodplain channel are now allowed to pour through breaches onto over 10,000 acres of formerly diked farmlands. The process started between 1980 and 2000 when Little Holland Tract (1456 acres) and Liberty Island (4340 acres) levees failed and were not repaired, leaving these lands open to the tides. Because these reclaimed wetlands had subsided during active farming, most of the “restored tidelands” became sub-tidal, year-round, warm, shallow, open-water habitat. Such habitat is too warm for Delta native fishes except during the winter.

The enhanced tidal exchange and warm productive winter and early-spring habitat attracts migratory Delta native fishes like smelt, splittail, and salmon to the Cache Slough Complex. While such habitat is considered beneficial in winter, it warms excessively in spring and summer, reducing the period of quality rearing, and can reduce overall survival and production. Native fishes have succumbed to the heat, stranding in the uneven landforms, and predation by non-native warm-water fish.

The latest projects, Lower Yolo Ranch (1749 acres), Yolo Flyway Farms (300 acres), and Lookout Slough (3000 acres), will add 5000 acres of mostly shallow intertidal habitat. Tidewater will flood onto these lands twice a day to warm in the California sun and then return to cooler deep, shaded, sub-tidal sloughs long considered prime Delta smelt and salmon rearing habitat. Not only will the new inter-tidal “wetlands” be too warm, but they will contribute to warming adjacent sub-tidal sloughs that convey water to and from other parts of the north Delta. This water quality degradation gets worse with each new project and has resulted in the degradation of the entire north Delta as a viable spawning, rearing, and critical habitat of Delta smelt. The effect has measurably contributed to the near extinction of Delta smelt.

The Evidence

The United States Geological Service has many water quality and flow monitoring gages in the Cache Slough Complex (Figure 2) that provide considerable evidence of the above-described problem. Specific gages with pertinent data records reviewed for this post are highlighted in Figure 2.

Waters in the northern Cache Slough Complex become too warm for salmon and smelt (>20ºC) by spring (Figure 3). In summer (Figure 4), water tidally flooded into subtidal island-tracts can warm 5-7ºC over a day before draining back into adjacent sloughs. Water temperatures in the northern sloughs of the Cache Slough Complex reach 25ºC (lethal to smelt) or higher in summer, even in wet and normal water years (2016-2018, Figure 5). Water temperatures in the southern Cache Slough Complex are only slightly lower (Figure 6). Over the past decade, water temperatures in the Cache Slough Complex overall have been gradually increasing (Figures 7 and 8), to the detriment of Delta native fishes.

The Solution

The problem can be lessened or even reversed at existing and future restoration projects by:

  1. Limiting tidal access to sub-tidal sites to winter, when water and air temperatures are colder.
  2. Building projects with flow-through tidal channel features rather than a single opening.
  3. Ensuring that projects are inter-tidal with small, narrow, shaded channels, or tule benches.
  4. Narrowing, deepening, and shading connecting tidal sloughs.
  5. Limiting discharge of warm agricultural wastewater into tidal channels.
  6. Providing supplementary inflow of Sacramento River water from the Fremont Weir, from the entrance gates of the Sacramento Deepwater Shipping Channel, or from other locations.
  7. Retrofitting existing restoration sites and designing future projects as outlined above.

 

Figure 2. USGS gage locations in the Cache Slough Complex.

Figure 3. Water temperatures recorded at Little Holland Tract in 2015-16.

Figure 4. Water temperatures and water surface elevation (gage height) recorded at Little Holland Tract in July 2017. Note higher water temperature spikes occurred with strongest ebb (draining) tides.

Figure 5. Water temperature in Liberty Cut adjacent to Little Holland Tract, 2016-18.

Figure 6. Water temperature and tidally-filtered flow rate in Sacramento Deepwater Ship Channel, April-September 2021.

Figure 7. Water temperature in lower Cache Slough, 2011-2016.

Figure 8. Water temperature in the lower Sacramento River channel near Rio Vista, 2010-2019.

Yolo Flyway Farms Tidal Wetland Restoration Project

Posted on by

Yolo Flyway Farms

The Yolo Flyway Farms project is a new element of the state’s EcoRestore program to fulfill requirements of federal biological opinions for the State Water Project and Central Valley Project. The 300-acre tidal wetland restoration project is located in the southern Yolo Bypass in what is commonly referred to as the Cache Slough Complex (Figure 1). The Project’s design entails allowing tidal access to excavated upland irrigated pasture land by opening levees along Prospect Slough (Figure 2). The Project is in a known area of concentration for Delta smelt as determined by nearby CDWR screw trap sampling in Prospect Slough (Figure 3). Project sponsors submitted a certification of consistency with the Delta Plan to the Delta Stewardship Council.1

Are such projects in the best interest of the Delta smelt population? A close look at project attributes may help answer the question.

Positive attributes:

  1. Replacement of the existing tide gate irrigation system with open levee breaches eliminates existing entrainment and loss of Delta smelt and other fishes into the irrigated pasture lands.
  2. New tidal channels and tidal wetlands would provide rearing habitat for young smelt, salmon, and splittail. Plankton and benthic invertebrate food sources for fish would likely increase.
  3. Hard surfaces may provide smelt spawning habitat.

Negative attributes:

  1. Tidal channels would provide new habitat for predatory birds and fish , which could increase loss of young smelt and salmon. Prospect Slough is deep, turbid, strong- current habitat unfavorable to predators. Tidal channels of project would be dead end, low velocity, less turbid habitats favorable to predators of fish.
  2. The southern Yolo Bypass aquatic habitats are warm from spring through fall, at times exceeding the thermal optimum for Delta smelt. Proposed shallow-water dead-end sloughs and flooded wetlands would warm and increase warming of Prospect Slough and other lower Bypass waters. While a positive attribute in winter and at times in late fall and early spring, this would be detrimental at other times.

Despite the potential positive benefits of such restoration in general, the potential negative aspects of the Project are a real concern. Some of the potential negative effects could be reduced through changes in project design and operations. At a minimum, the project should be considered an adaptive management experiment where potential positive and negative attributes are studied to determine the overall benefit of the action and whether it fulfills the objectives of the biological opinions.

Figure 1. Yolo Flyway Farms Project location (red circle) in southern Yolo Bypass.

Figure 3. Prospect Slough adjacent to Deepwater Shipping Channel and Liberty Island in southern Yolo Bypass. CDWR screw trap in yellow circle.

Over-Summering Spring-Run Chinook Salmon in Mill Creek and Deer Creek

Posted on by

In a recent research paper, authors Cordoleani, Phillis, and Sturrock describe what they call a “rare” life history of spring-run Chinook salmon in Mill Creek and Deer Creek, tributaries to the Sacramento River. The authors suggest that this life history is becoming increasingly important in our warming climate.1 For more discussion of this topic, see also:  https://fishbio.com/worth-waiting-for-the-advantages-of-late-migrating-spring-run-chinook/. The authors’ abstract for the paper provides the following summary:

ABSTRACT: Rare phenotypes and behaviours within a population are often overlooked, yet they may serve a heightened role for species imperilled by rapid warming. In threatened spring-run Chinook salmon spawning at the southern edge of the species range, we show late-migrating juveniles are critical to cohort success in years characterized by droughts and ocean heatwaves. Late migrants rely on cool river temperatures over summer, increasingly rare due to the combined effects of warming and impassable dams. Despite the dominance of late migrants, other strategies played an important role in many years. Our results suggest that further loss of phenotypic diversity will have critical impacts on population persistence in a warming climate. Predicted thermally suitable river conditions for late migrants will shrink rapidly in the future and will be largely relegated above impassable dams. Reconnecting diverse habitat mosaics to support phenotypic diversity will be integral to the long-term persistence of this species.

What the authors of this study are noting is the two dominant life history patterns of Chinook salmon: subyearling and yearling smolt production, or “ocean” type vs. “river” type Chinook. One type or the other often dominates in a particular river system, but often both types exist, providing for a diversity of life history that protects the species from extinction.

The main difference is that the subyearling or ocean type leaves for the ocean, estuaries, and coastal waters in late winter or spring, whereas the river type over-summers in rivers before emigrating to the ocean in the following fall or winter.

Technically speaking, neither “type,” “behavior,” or “strategy” is “rare” (or “overlooked”). The ocean type occurs in many river systems, especially in the Chinook salmon’s southern range, which provides conditions for rapid winter growth that allows young salmon to reach smolt size by spring – “early” outmigrants. Slow growth, more common in the colder northern range of Chinook, often requires young salmon to “over-summer” in rivers to reach smolt size to migrate to the ocean.

Spring-run Chinook have adapted to colder, higher elevation streams, especially in their southern range in California’s Central Valley. In contrast, fall-run Chinook spawn in lower elevation streams or lower portions of coastal, Central Valley, and Klamath-Trinity rivers. The spring-run tend to be more river type because of the colder water and longer journeys, whereas fall-run are faced with warmer water and shorter journeys. Fall-run also tend to rear in estuaries.

In Central Valley rivers, most of the historical populations of spring-run Chinook have been cut off from the higher elevation spawning reaches. They are forced to spawn below rim dams, and populations specific to many rivers (such as the American) have not survived. For populations that survive downstream of rim dams, the ocean type strategy pre-dominates, though in the coldest tailwaters of rim dams, some over-summering is possible, and the river type life history occurs for both spring-run and fall-run Chinook. In drought years, tailwaters may become too warm, and river type smolt production suffers.

In Central Valley rivers where no major dams occur, such as Mill Creek and Deer Creek, both life history strategies occur. The authors document that more than half of the adult spring-run sampled over a 12-year period that returned to Mill and Deer creeks had emigrated from their natal streams using a river type life history. The trend was more pronounced for drought years.

The authors emphasize the importance of cold-water habitats in higher-elevation rivers and the river type life history for spring-run Chinook as the climate warms. Yet there are additional factors that should be considered in evaluating why the spring-run populations in Mill and Deer Creek are so heavily dependent on the river type life history. These other factors are related to lack of rearing habitat in the lower reaches of these streams and to the dependence of their outmigrating juvenile salmon on flows, including in the Sacramento River.

A look at the CDFW Grand Tab for escapement of Central Valley spring-run Chinook (pp. 8-9) shows Mill Creek and Deer Creek haven’t reached 1000 adult fish returning to either stream since 2006. In contrast, returns to Butte Creek are perennially in the thousands. and in four years since 2006 topped 10,000. In large part, this is because there is abundant rearing habitat in the Butte Sink and Sutter Bypass complex for Butte Creek spring-run juveniles. Mill Creek and Deer Creek don’t have substantial low-elevation rearing habitat accessible to juvenile spring-run.

So while the river type life history appears to be a viable strategy to help save the spring-run populations in Mill Creek and Deer Creek from extinction, it has not yet shown itself to be a viable strategy for recovery comparable to the elements present on Butte Creek.

Reports by the California Department of Fish and Wildlife (formerly Fish and Game ) document the relative success of the river type life history for spring-run juveniles in Butte Creek.2 However, successful returns of river type spring-run in Butte Creek (measured in single digits) are grossly overshadowed by overall escapement.

A major common trait of spring-run Chinook that survive to escapement, both among river type spring-run in Mill Creek and Deer Creek, and among ocean type and river type spring-run in Butte Creek, is that they are well positioned to emigrate to the Delta and Bay as large smolts in the December-March time period. This is the most likely time for flows in the Sacramento River that have sufficient magnitude to allow successful downstream migration and rearing in the Sacramento and the Delta. It is also necessary in all three of these tributaries to the Sacramento, because agricultural diversions ramp up substantially in mid-April, and flows on the valley floor in these streams then become much more difficult to navigate than before April.

In summary, the authors’ characterization of the “river” strategy as “rare,” especially for spring-run Chinook, is not accurate. Nonetheless, the difficulty of maintaining the river type life history strategy because of drought and global warming for Central Valley spring-run and fall-run Chinook is increasing on the valley floor. Furthermore, the “ocean” strategy for both spring-run and fall-run Chinook suffers the most from drought and global warming as the rearing and emigration windows of the lower rivers and estuary shrink.

Improved access to thermally suitable higher elevation streams, including habitat upstream of rim dams, is going to be essential under a warming climate in the future. A river type life history may play an increasing part. However, the contrasts in escapement of spring-run Chinook between Mill and Deer Creeks on the one hand, and Butte Creek on the other, show the importance of also establishing and maintaining connectivity to quality rearing habitats on or near the valley floor. Migration habitat, or sufficient flows in the lower reaches of the Sacramento River and its tributaries, is a third key element of recovering spring-run and other runs of Central Valley Chinook salmon.

  1. Cordoleani, F., Phillis, C.C., Sturrock, A.M. et al.Threatened salmon rely on a rare life history strategy in a warming landscape.  Clim. Chang.11, 982–988 (2021). https://doi.org/10.1038/s41558-021-01186-4. ↩
  2. See, e.g., Ward, P.D., McReynolds T.R., and Garman, C.E., Spring-Run Chinook Salmon, Oncorhynchus Tshawytscha, Life History Investigation 2002-2003, 2004, DFW Ref # 90573, p. 2: “The limited sample suggests that However, the yearling Butte Creek spring-run survive at a rate significantly higher than YOY emigrants.”  Available at: https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjNmuCEh_b3AhX0KkQIHYIDA6cQFnoECAYQAQ&url=https%3A%2F%2Fnrm.dfg.ca.gov%2FFileHandler.ashx%3FDocumentID%3D32894&usg=AOvVaw28r2uoKbLqAvzrCljBoX7A.  See also McReynolds, et al CDFW, Butte and Big Chico Creeks, Spring-Run Chinook Salmon, Oncoryhnchus Tshawytscha, Life History Investigation 2004-2005, 2006, Ref # 90754, Table 1 p. 9. Shows yearling outmigrants trapped in 2004. See also Appendix B, figure 1.  Available at: https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&ved=2ahUKEwic4J20mvf3AhVZoY4IHaqGCu8QFnoECAQQAQ&url=https%3A%2F%2Fnrm.dfg.ca.gov%2FFileHandler.ashx%3FDocumentID%3D32895&usg=AOvVaw2Z7RFTthJ03e6d0IkW0by2. ↩

State and Federal Hatcheries Release Salmon Smolts to Rivers, Delta, Bay, and Coast

Posted on by

Hatcheries in California are releasing tens of millions of salmon smolts in 2022, per normal operations.  State hatcheries are trucking over ten million fall-run salmon to the Bay again this spring because of the drought.  State and federal hatcheries are releasing another ten million-plus fall-run smolts to the rivers near the hatcheries.

Future salmon fisheries will depend mostly on the Bay releases, because few of the hatchery smolts released to the river or wild salmon smolts will survive the journey to the ocean this drought year.  Yet even the prognosis for smolts released to the Bay is poor.  Delta outflows near 4000 cfs under the State’s TUCP will keep survival below one percent (Figure 1).

Meanwhile, the prognosis for wild fall-run smolts under the TUCP is grim as they began moving through the Delta in late April and early May (Figures 2 and 3).  The extra month of normal outflow needed to help the salmon get to the ocean would amount to about 100-150 TAF, less than 10% of what is being supplied to water users from reservoirs in spring 2022.  Is the TUCP allocation to outflow and fish reasonable?

Figure 1. Fall-run salmon adult returns to the American River hatchery from Bay releases vs Delta outflow to Bay at time of release. Years noted are percent returns for below normal years 2016 and 2018, and wet year 2017 under normal rules. Blue dots with outflow below 5000 cfs are from 2014 and 2015, TUCP years. Red line is hypothesized relationship. Returns under normal rules are approximately triple the returns under TUCP rules.

Figure 2. Red circle denotes wild fall-run and spring-run smolts passing through the Delta in late April and early May 2022.

Figure 3. Peak migration of fall-run and spring-run smolts into Bay from Delta in late April and early May 2022.