Chapter 5 Middle and Lower Sacramento Juveniles

This section describes environmental attributes associated with and responses during the out-migrating juvenile life stage in the Lower and Middle Sacramento River.

5.1 Habitat Attributes

  1. Habitat Capacity (Floodplain Connectivity)

  2. Habitat Capacity: Depth/Shallow Water

  3. In-Stream Habitat Capacity

5.1.1 Storage and Flows

  1. Shasta Storage/Hydrology

  2. Flows: Migration Cues

5.1.1.1 Flow Conditions on the Middle and Lower Sacramento River

Figure 5.1: Daily Flows (cfs) at Sacramento River at Hamilton City (HMC), Sacramento River at Wilkins Slough (WLK) and Sacramento River at Verona (VON) from September 2021 through March 2022 and over the 10-year average

Table 5.1: Mean, Maximum and Minimum Monthly Flows (cfs) at Sacramento River at Hamilton City (HMC), Sacramento River at Wilkins Slough (WLK) and Sacramento River at Verona (VON) from September 2021 through March 2022
Year Month Station Mean Min Max
2021 September HMC 5885.7 5590 6182
2021 October HMC 13842.8 5945 47509
2021 November HMC 7181.8 3983 17544
2021 December HMC 11421.0 3400 29442
2022 January HMC 7669.2 4678 12005
2022 February HMC 4326.8 3744 4934
2022 March HMC 3983.1 3615 4333
2021 September WLK 5605.0 5290 5920
2021 October WLK 11000.4 5650 25100
2021 November WLK 7160.0 4370 12700
2021 December WLK 9375.3 3990 20600
2022 January WLK 7715.4 5190 12000
2022 February WLK 4732.0 4060 5400
2022 March WLK 4200.0 3930 4470
2021 September VON 7827.2 7160 8420
2021 October VON 18089.0 7110 35500
2021 November VON 8051.0 5480 12900
2021 December VON 15431.8 5500 31900
2022 January VON 14467.4 9010 23200
2022 February VON 10197.1 9610 11500
2022 March VON 8856.6 7490 11200

5.1.1.2 Juvenile WRCS Rescued During Stranding Surveys

Fish were not stranded in the Middle to Lower Sacramento River for Brood Year 2021.

Summary

  • Hamilton City: Peak flows were 47509 cfs and occurred in October. The highest mean flows were 13842.8 cfs and occurred in October.

  • Wilkins Slough: Peak flows were 25100 cfs and occurred in October. The highest mean flows were 11000.4 cfs and occurred in October.

  • Verona: Peak flows were 35500 cfs and occurred in October. The highest mean flows were 18089 cfs and occurred in October.

5.1.2 Environmental Drivers

5.1.2.1 Turbidity

Figure 5.2: Daily Turbidity at Red Bluff Diversion Dam (RDB) and Sacramento River at Freeport (FPT) from September 2021 through March 2022

Table 5.2: Mean, Maximum, Minimum Monthly Flows (cfs) at Red Bluff Diversion Dam (RDB) and Sacramento River at Freeport (FPT) from September 2021 through March 2022
Year Month Station Mean Min Max
2021 September RDB 8.8 6.0 11.5
2021 October RDB 9.5 5.2 13.2
2021 November RDB 8.6 6.4 10.9
2021 December RDB 10.3 5.9 14.5
2022 January RDB 14.0 11.1 16.9
2022 February RDB 14.4 11.4 17.3
2022 March RDB 9.7 4.3 15.3
2021 September FPT 2.6 0.8 5.2
2021 October FPT 47.7 1.0 123.0
2021 November FPT 10.1 3.4 24.0
2021 December FPT 44.2 2.3 107.0
2022 January FPT 14.5 1.6 30.3
2022 February FPT 7.3 3.0 11.8
2022 March FPT 5.1 1.8 10.1

Summary

  • Red Bluff Diversion Dam: Minimum turbidity was 4.3 FNU and occurred in March. The lowest mean turbidity was 8.6 FNU and occurred in November.
  • Sacramento River at Freeport: Minimum turbidity was 0.8 FNU and occurred in September. The lowest mean turbidity was 2.6 FNU and occurred in September.

5.1.2.2 Water Temperature

Table 5.3: Mean, Maximum, Minimum Monthly Water Temperature (°F) at Sacramento River Below Wilkins Slough (WLK) in September 2021 through March 2022 . Days > 63°F indicates the number of days per month that experienced at least 1 hour where Water Temperature was greater than 63°F.
Year Month Station Mean Min Max Water Temp < 63 Degf
2021 September WLK 69.5 63.8 90.7 30
2021 October WLK 61.2 57.3 71.7 8
2021 November WLK 56.8 52.4 62.0 0
2021 December WLK 49.7 45.1 54.9 0
2022 January WLK 48.7 44.8 51.0 0
2022 February WLK 51.9 47.0 56.7 0
2022 March WLK 58.8 53.0 66.7 8

Summary

  • Maximum water temperature was 90.7 degrees F and occurred in September. The highest mean water temperature was 69.5 degrees F and occurred in September.
  • The month with greatest days exceeding 63 degrees F (30 days) was September.

5.1.2.3 Dissolved Oxygen

Table 5.4: Mean, Maximum, Minimum Monthly Flows (cfs) at Red Bluff Diversion Dam (RDB) and Sacramento River at Hood (SRH) in 2021 - 2022 . Days less than 6 mg/L indicates the number of days per month that experienced at least 1 hour where DO was less than 6 mg/L.
Year Month Station Mean Min Max Do < 6mg/L
2021 September RDB 8.4 6.0 11.5 0
2021 October RDB 9.9 5.2 13.2 5
2021 November RDB 8.5 6.4 10.9 0
2021 December RDB 10.2 5.9 14.5 1
2022 January RDB 14.2 11.1 16.9 0
2022 February RDB 14.5 11.4 17.3 0
2022 March RDB 8.3 4.3 15.3 17
2021 September SRH 8.2 7.6 9.2 0
2021 October SRH 8.8 6.4 10.0 0
2021 November SRH 8.9 7.1 10.1 0
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

Summary

  • Sacramento River at Bend Bridge: Minimum dissolved oxygen was 4.3 mg/L and occurred in March. The lowest mean dissolved oxygen was 8.3 mg/L and occurred in March.
  • Sacramento River at Hood: Minimum dissolved oxygen was 6.4 mg/L and occurred in October. The lowest mean dissolved oxygen was 8.2 mg/L and occurred in September.

5.2 Biological Response

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)

Data Sources

  • JPE, Smolt survival from JPE Letters (link)

5.2.1 Juvenile Production Estimate (Abundance)

Total Natural production entering the Delta (JPE)

Figure 5.3: Total Natural production entering the Delta (JPE)

Total Hatchery Production entering the Delta (Hatchery JPE)

Figure 5.4: Total Hatchery Production entering the Delta (Hatchery JPE)

5.2.2 Smolt Survival

5.2.2.1 JPE Letter

Natural-origin smolt survival is calculated at the Tower Bridge from acoustically tagged hatchery fish that are released at RBDD.

Natural-origin Smolt Survival from RBDD to Tower Bridge. A new calculation method was implemented for BY 2019, resulting in lower estimates. Prior to 2013 a constant value of 0.54 was used.

Figure 5.5: Natural-origin Smolt Survival from RBDD to Tower Bridge. A new calculation method was implemented for BY 2019, resulting in lower estimates. Prior to 2013 a constant value of 0.54 was used.

5.2.2.2 Acoustic Tagging

Reach-specific survival

Table 5.5: Table of Hatchery WR Juvenile Survival
rel_date reach_start reach_end rkm_start ReachSurvival CumulativeSurvival count
2022-02-10 Caldwell_Park_Rel Blw_Cypress 551 0.995 (0.988, 0.998) 1 (0, 0) 139
2022-02-10 Blw_Cypress Blw_ClearCr 544 0.999 (0.994, 1) 0.964 (0.92, 0.98) 134
2022-02-10 Blw_ClearCr BlwCowCr 536 0.999 (0.996, 1) 0.957 (0.91, 0.98) 133
2022-02-10 BlwCowCr Battle_Conf 521 0.999 (0.995, 1) 0.95 (0.9, 0.98) 132
2022-02-10 Battle_Conf Blw_Paynes_Ck 507 0.997 (0.995, 0.999) 0.935 (0.88, 0.97) 130
2022-02-10 Blw_Paynes_Ck Blw_Salt 476 0.996 (0.992, 0.998) 0.863 (0.8, 0.91) 120
2022-02-10 Blw_Salt Mill_Ck_Conf 457 0.999 (0.99, 1) 0.799 (0.72, 0.86) 111
2022-02-10 Mill_Ck_Conf Ord 441 0.992 (0.989, 0.994) 0.782 (0.7, 0.85) 106
2022-02-10 Ord Colusa AC2 372 0.989 (0.984, 0.993) 0.449 (0.36, 0.54) 57
2022-02-10 Colusa AC2 AbvColusaBr 319 0.998 (0.978, 1) 0.252 (0.19, 0.33) 35
2022-02-10 AbvColusaBr Colusa BC2 308 0.998 (0.947, 1) 0.245 (0.18, 0.32) 31
2022-02-10 Colusa BC2 AbvTisdale 296 0.997 (0.988, 0.999) 0.241 (0.18, 0.32) 26
2022-02-10 AbvTisdale Knights_RST 269 0.995 (0.99, 0.998) 0.224 (0.16, 0.3) 30
2022-02-10 Knights_RST Abv_FremontWeir 222 0.995 (0.952, 0.999) 0.18 (0.12, 0.25) 25
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 NA NA 167 NA (NA, NA) 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
2022-02-10 NA NA 2 NA (NA, NA) 0.065 (0.03, 0.12) 2
2022-03-02 Caldwell_Park_Rel Blw_Cypress 551 0.996 (0.993, 0.998) 1 (0, 0) 430
2022-03-02 Blw_Cypress Blw_ClearCr 544 0.999 (0.997, 1) 0.972 (0.95, 0.98) 418
2022-03-02 Blw_ClearCr BlwCowCr 536 1 (0.999, 1) 0.963 (0.94, 0.98) 414
2022-03-02 BlwCowCr Battle_Conf 521 0.998 (0.997, 0.999) 0.958 (0.94, 0.97) 412
2022-03-02 Battle_Conf Blw_Paynes_Ck 507 0.997 (0.996, 0.998) 0.935 (0.91, 0.96) 402
2022-03-02 Blw_Paynes_Ck Blw_Salt 476 0.997 (0.995, 0.998) 0.856 (0.82, 0.89) 368
2022-03-02 Blw_Salt Mill_Ck_Conf 457 0.993 (0.99, 0.996) 0.8 (0.76, 0.84) 344
2022-03-02 Mill_Ck_Conf Ord 441 0.988 (0.986, 0.99) 0.722 (0.67, 0.77) 291
2022-03-02 Ord Colusa AC2 372 0.991 (0.988, 0.994) 0.315 (0.27, 0.36) 116
2022-03-02 Colusa AC2 AbvColusaBr 319 0.99 (0.981, 0.995) 0.198 (0.16, 0.24) 85
2022-03-02 AbvColusaBr Colusa BC2 308 0.997 (0.987, 0.999) 0.178 (0.14, 0.22) 68
2022-03-02 Colusa BC2 AbvTisdale 296 0.999 (0.995, 1) 0.171 (0.14, 0.21) 61
2022-03-02 AbvTisdale Knights_RST 269 0.998 (0.996, 0.999) 0.166 (0.13, 0.2) 69
2022-03-02 Knights_RST Abv_FremontWeir 222 0.998 (0.981, 1) 0.153 (0.12, 0.19) 66
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 NA NA 167 NA (NA, NA) 0.116 (0.09, 0.15) 50
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
2022-03-02 NA NA 2 NA (NA, NA) 0.056 (0.04, 0.08) 11

5.2.3 Migration Timing

Cumulative Raw Catch: RBDD, Chipps, Tisdale, Knights, Sac Beach Seines, Sac Trawls
Raw Juvenile Rotary Screw Trap Cumulative Catch

Figure 5.6: Raw Juvenile Rotary Screw Trap Cumulative Catch

Median Passage Dates

Migration Timing

Knights Landing Rotary Screw Trap Migration Timing

Figure 5.7: Knights Landing Rotary Screw Trap Migration Timing

Sacramento Trawl Timing

Figure 5.8: Sacramento Trawl Timing

5.2.4 Condition

Do we want FL on any surveys?