Chapter 6 Sacramento-San Joaquin Delta Juveniles

This section describes environmental attributes associated with and responses during the out-migrating juvenile life stage in the Sacramento-San Joaquin Delta.

6.1 Habitat Attributes

  1. Rearing Habitat Capacity (Floodplain Connectivity)
  • Weir overtopping

6.1.1 Food Availability

Zooplankton Abundance in the Delta, December 2021 - June 2022 and 10-year average CPUE

Figure 6.1: Zooplankton Abundance in the Delta, December 2021 - June 2022 and 10-year average CPUE

Amphipod and Mysid Abundance in the Delta, December 2021 and 10-year average CPUE. Data currently include only EMP data from December 2021

Figure 6.2: Amphipod and Mysid Abundance in the Delta, December 2021 and 10-year average CPUE. Data currently include only EMP data from December 2021

6.2 Environmental Drivers

6.2.1 Sacramento River Flow and Delta Outflow

Table 6.1: Sacramento River at Freeport (FPT), Delta Outflow (DTO), Old and Middle River (OMR) Mean, Maximum, Minimum Monthly Flows (cfs) in 2021 - 2022
Year Month Station Mean Min Max
2021 December FPT 8616.8 -5360 36600
2022 January FPT 12824.9 1370 32600
2022 February FPT 8173.3 2880 17200
2022 March FPT 6008.5 -1390 17000
2022 April FPT 4295.7 -3630 15700
2022 May FPT 3310.5 -4040 15300
2022 June FPT 4553.0 -2710 18300
2021 December DTO 18383.4 2674 45494
2022 January DTO 13135.7 5266 33374
2022 February DTO 11724.5 11150 12147
2022 March DTO 9559.9 5712 12035
2022 April DTO 7716.9 4865 11825
2022 May DTO 4553.6 3082 5697
2022 June DTO 4936.1 3937 6935
2021 December OMR -2738.9 -9193 -86
2022 January OMR -4493.8 -5631 -1289
2022 February OMR -1688.3 -4780 -389
2022 March OMR -1919.8 -3776 191
2022 April OMR -981.3 -2710 2423
2022 May OMR -1690.0 -3774 2519
2022 June OMR -1922.2 -3400 2523

Figure 6.3: Freeport (FPT) Average Flows (cfs) in 2021 and over the 10-year average

Figure 6.4: Delta Outflow (DTO) in 2021 and over the 10-year average

Figure 6.5: OMR Flow (OMR) (cfs) in 2021 and over the 10-year average

Summary

  • Sacramento River at Freeport: Peak flows were 3.66^{4} cfs and occurred in December. The highest mean flows were 1.28249^{4} cfs and occurred in January. Flow was generally lower than average.

  • Delta Outflow: Peak Delta outflow was 4.5494^{4} cfs and occurred in December. The highest mean Delta outflow was 1.83834^{4} cfs and occurred in December. Flow was generally lower than average.

  • Old and Middle River: The most negative OMR flows were -9193 cfs and occurred in December. The most negative mean OMR flows were -4493.8 cfs and occurred in January. OMR was generally similar to average.

6.2.2 Water Temperature

Table 6.2: FPT (Sacramento River at Freeport), SUS (Steamboat Slough below Sutter Slough), SWE (Sacramento River at Walnut Grove), GSS (Georgiana Slough at Sacramento River), MAL (Sacramento River at Mallard Island) Mean, Maximum, Minimum Monthly Water Temperature (°F) in 2021 - 2022
Year Month Station Mean Min Max Days > 57.2 Degf Days > 63 Degf
2021 December FPT 49.6 45.9 55.4 0 0
2022 January FPT 48.6 45.7 50.0 0 0
2022 February FPT 51.6 47.5 55.0 0 0
2022 March FPT 57.9 52.9 64.9 17 5
2022 April FPT 62.7 58.8 67.6 30 16
2022 May FPT 68.8 62.2 75.2 31 31
2022 June FPT 73.3 69.6 77.9 29 29
2021 December SUS 50.2 45.9 54.7 0 0
2022 January SUS 48.8 45.7 50.5 0 0
2022 February SUS 51.8 47.7 55.8 0 0
2022 March SUS 58.2 51.8 64.9 18 7
2022 April SUS 63.1 59.9 68.0 30 23
2022 May SUS 69.2 63.7 75.2 31 31
2022 June SUS 74.1 70.9 77.9 30 30
2021 December SWE 50.1 45.9 54.5 0 0
2022 January SWE 48.7 45.7 50.4 0 0
2022 February SWE 51.7 47.8 54.5 0 0
2022 March SWE 57.9 52.0 64.0 16 5
2022 April SWE 62.8 59.9 66.7 30 17
2022 May SWE 68.8 63.9 73.4 31 31
2022 June SWE 73.6 70.7 76.8 30 30
2021 December GSS 50.2 46.0 54.7 0 0
2022 January GSS 48.9 45.9 55.4 0 0
2022 February GSS 51.9 47.8 55.2 0 0
2022 March GSS 58.0 52.0 64.2 17 6
2022 April GSS 63.0 56.3 66.9 30 19
2022 May GSS 69.0 64.0 75.9 31 31
2022 June GSS 73.8 70.9 77.0 30 30
2021 December MAL 52.4 47.6 57.8 3 0
2022 January MAL 49.2 47.1 51.7 0 0
2022 February MAL 51.9 49.6 54.9 0 0
2022 March MAL 57.0 53.0 61.3 18 0
2022 April MAL 61.5 59.0 64.1 30 7
2022 May MAL 64.6 61.0 71.1 31 27
2022 June MAL 70.1 66.3 75.1 30 30

Summary

  • Maximum water temperature was 77.9 °F and occurred in June. The highest mean water temperature was 73.3 °F and occurred in June.

  • Maximum water temperature was 77.9 °F and occurred in June. The highest mean water temperature was 74.1 °F and occurred in June.

  • Maximum water temperature was 77 °F and occurred in June. The highest mean water temperature was 73.8 °F and occurred in June.

  • Maximum water temperature was 75.1 °F and occurred in June. The highest mean water temperature was 70.1 °F and occurred in June.

  • Temperature Exceedances:

    • 57.2°F: Upper range of optimal rearing temperature for juvenile Chinook Salmon (Windell et al. 2017)
    • 63°F: Temperature at which smolt development is inhibited (Windell et al. 2017)
    • Water temperature exceeded optimal rearing temperature consistently (14 days or more) starting in March for FPT, March for SUS, March for SWE, March for GSS, and March for MAL
    • Water temperature reached temperature at which smolt development is inhibited consistently starting in `r March for FPT, March for SUS, March for SWE, March for GSS, and April for MAL

6.2.3 Dissolved Oxygen

Table 6.3: SRH (Sacramento River at Hood), SXS (Steamboat Slough near Sacramento River), BLP (Blind Point), MAL (Sacramento River at Mallard Island) Mean, Maximum, Minimum Monthly DO (mg/L) in 2021 - 2022
Year Month Station Mean Min Max Days < 6 Mg/L
2021 December SRH 10.1 9.5 10.7 0
2022 January SRH 11.0 10.6 11.4 0
2022 February SRH 10.9 10.2 11.7 0
2022 March SRH 9.9 8.5 11.1 0
2022 April SRH 9.0 8.3 9.6 0
2022 May SRH 8.5 7.9 10.5 0
2022 June SRH 8.1 7.5 9.1 0
2021 December SXS 9.7 9.2 10.4 0
2022 January SXS 10.7 10.2 11.2 0
2022 February SXS 10.9 9.7 12.5 0
2022 March SXS 10.3 8.5 12.5 0
2022 April SXS 9.4 8.6 10.7 0
2022 May SXS 8.9 7.5 11.9 0
2022 June SXS 8.1 7.1 9.2 0
2021 December BLP 9.5 8.3 10.4 0
2022 January BLP 9.8 9.3 10.5 0
2022 February BLP 10.6 9.8 10.9 0
2022 March BLP 10.3 9.2 11.2 0
2022 April BLP 9.4 8.6 10.4 0
2022 May BLP 9.0 8.0 10.1 0
2022 June BLP 8.4 7.7 9.9 0
2021 December MAL 9.4 8.2 10.4 0
2022 January MAL 10.1 9.6 10.6 0
2022 February MAL 10.3 9.8 10.6 0
2022 March MAL 10.1 9.3 10.9 0
2022 April MAL 9.3 8.8 10.0 0
2022 May MAL 8.9 8.3 9.4 0
2022 June MAL 8.4 7.7 9.1 0

Summary

  • Minimum dissolved oxygen was 7.5 mg/L and occurred in June. The lowest mean dissolved oxygen was 8.1 mg/L and occurred in June. DO did not reach values below 6mg/L.
  • Minimum dissolved oxygen was 7.1 mg/L and occurred in June and NA. The lowest mean dissolved oxygen was 8.1 mg/L and occurred in June. DO did not reach values below 6mg/L.
  • Minimum dissolved oxygen was 7.7 mg/L and occurred in June. The lowest mean dissolved oxygen was 8.4 mg/L and occurred in June. DO did not reach values below 6mg/L.
  • Minimum dissolved oxygen was 7.7 mg/L and occurred in June. The lowest mean dissolved oxygen was 8.4 mg/L and occurred in June. DO did not reach values below 6mg/L.

6.3 Biological Response

6.3.1 Survival

6.3.1.1 Hatchery Releases

Hatchery WRCS are released each year from Caldwell Park. Releases for BY 2021 occurred in February and March. - Cumulative survival from release to Benicia Bridge (6.4) - Release 1: Reach survival estimates ranged from 0.989 to 1 - Release 2: Reach survival estimates ranged from 0.985 to 1

Table 6.4: Table of Hatchery WR Juvenile Survival
rel_date reach_start reach_end rkm_start ReachSurvival CumulativeSurvival count
2022-02-10 Abv_FremontWeir SacFeather 215 0.995 (0.965, 0.999) 0.174 (0.12, 0.25) 21
2022-02-10 SacFeather Blw_Elkhorn_GS1 206 1 (1, 1) 0.165 (0.11, 0.24) 22
2022-02-10 Blw_Elkhorn_GS1 TowerBridge 192 0.998 (0.984, 1) 0.165 (0.11, 0.24) 23
2022-02-10 TowerBridge SacTrawl 172 1 (1, 1) 0.158 (0.11, 0.23) 22
2022-02-10 Freeport Abv_Clarksburg 152 1 (1, 1) 0.137 (0.09, 0.2) 19
2022-02-10 Abv_Clarksburg Hood 148 1 (1, 1) 0.137 (0.09, 0.2) 19
2022-02-10 Hood Chipps 138 0.992 (0.984, 0.996) 0.137 (0.09, 0.2) 19
2022-02-10 Chipps Benicia 71 0.989 (0.959, 0.997) 0.08 (0.04, 0.14) 11
2022-02-10 Benicia GoldenGateE 52 1 (1, 1) 0.065 (0.03, 0.12) 9
2022-03-02 Abv_FremontWeir SacFeather 215 0.998 (0.985, 1) 0.151 (0.12, 0.19) 58
2022-03-02 SacFeather Blw_Elkhorn_GS1 206 0.996 (0.989, 0.999) 0.149 (0.12, 0.19) 61
2022-03-02 Blw_Elkhorn_GS1 TowerBridge 192 0.994 (0.987, 0.997) 0.142 (0.11, 0.18) 61
2022-03-02 TowerBridge SacTrawl 172 0.985 (0.961, 0.994) 0.126 (0.1, 0.16) 54
2022-03-02 Freeport Abv_Clarksburg 152 0.991 (0.964, 0.998) 0.107 (0.08, 0.14) 46
2022-03-02 Abv_Clarksburg Hood 148 0.995 (0.981, 0.999) 0.102 (0.08, 0.14) 44
2022-03-02 Hood Chipps 138 0.993 (0.989, 0.996) 0.098 (0.07, 0.13) 42
2022-03-02 Chipps Benicia 71 0.994 (0.981, 0.998) 0.063 (0.04, 0.09) 26
2022-03-02 Benicia GoldenGateE 52 1 (1, 1) 0.056 (0.04, 0.08) 24

Figure 6.6: Cumulative Survival by River Kilometer

6.3.1.2 Modeled Survival and Routing (STARS)

  • Survival summary
  • Routing summary

6.3.2 Abundance

Catch for all surveys

Summary

  • Juvenile WRCS cumulative total catch:
    • Sacramento Trawls at Sherwood Harbor: 22 (Index = 22)
    • Sacramento Beach Seines: 23 (Index = 50.2)
    • Chipps Island Trawl: 10
  • Migration Timing:
    • Delta Entry (Sacramento Trawls at Sherwood Harbor):
      • First: October 27, 2021
      • Median: June 18, 2021
      • Last: February 23, 2022
    • Delta Exit (Chipps Island Trawl):
      • First: November 01, 2021
      • Median: June 18, 2021
      • Last: April 05, 2022

6.3.3 Migration Timing

Sac Trawl Data (Raw Catch by Day or Week?)

SacPAS Migration Timing Table - LAD Median Dates, 10 Year Comparison Sacramento Beach Seines, Trawls, Chipps Island Trawls

Combined Beach Seines Migration Timing

Figure 6.7: Combined Beach Seines Migration Timing

Delta Exit (Chipps Island) Migration Timing

Figure 6.8: Delta Exit (Chipps Island) Migration Timing

6.3.4 Condition

Plot of current year sizes for Salvage, Chipps, Sacramento Beach Seines, Sac Trawls at Sherwood

Fork Lengths of Genetic and LAD Winter Run Chinook Salmon Juveniles at Salvage. Points indicate median fork length.

(#fig:salvage_fl-fig)Fork Lengths of Genetic and LAD Winter Run Chinook Salmon Juveniles at Salvage. Points indicate median fork length.

Fork Lengths of Genetic and LAD Winter Run Chinook Salmon Juveniles at Chipps Trawl. Points indicate median fork length.

(#fig:chipps_fl-fig)Fork Lengths of Genetic and LAD Winter Run Chinook Salmon Juveniles at Chipps Trawl. Points indicate median fork length.

6.3.5 Entrainment

  • Describe take levels based off JPE letter
  • Describe trigger levels
  • Describe loss

Salvage Timing

Salvage Timing

Figure 6.9: Salvage Timing

Winter-run Current and Historic Cumulative Salvage (Line plots)

6.3.5.1 Historical Loss

Summary

  • Total LAD loss for BY 2021 was 73.04, which was 0.0005841424% of the JPE. Loss was lower than the 10-year average of 284.16 (Figure 6.10.

  • Total Genetic loss for BY 2021 was 0, which was 0% of the JPE. Loss was lower than the 10-year average of 92.65 (Figure 6.11.

Genetic vs Length-At-Date (LAD) Winter Run Chinook Salmon Loss through 2021. Genetic loss data provided by USBR before WY 2020. LAD and genetic loss after 2020 sourced from CDFW Salvage Database.

Figure 6.10: Genetic vs Length-At-Date (LAD) Winter Run Chinook Salmon Loss through 2021. Genetic loss data provided by USBR before WY 2020. LAD and genetic loss after 2020 sourced from CDFW Salvage Database.

6.3.5.2 Loss as a Percent of JPE

Genetic vs Length-At-Date (LAD) Winter Run Chinook Salmon Percent Loss of JPE through 2021. Genetic loss data provided by USBR before WY 2020. LAD and genetic loss after 2020 sourced from CDFW Salvage Database.

Figure 6.11: Genetic vs Length-At-Date (LAD) Winter Run Chinook Salmon Percent Loss of JPE through 2021. Genetic loss data provided by USBR before WY 2020. LAD and genetic loss after 2020 sourced from CDFW Salvage Database.

Monitoring Sources for abundance, growth/size, migration timing/duration

  • Sac Trawl

  • Tisdale Weir

  • Knights Landing

  • GCID

  • DJFMP

  • Yolo Bypass

  • Chipps Island Trawl (Exit)

  • Genetic (Chipps, SWP/CVP, Knights Landing, Yolo Bypass)

  • Hatchery real-time: Calfish Track/ERDDAP

  • Natural Origin Smolt survival (O Farell et al. 2018)

  • Hatchery Origin Smolt survival

  • Modeled: ** Juvenile: STARS ** Fish Model

  • Survival to Delta: Production (Hatchery JPE, Modeled JPE)