Reorienting to Recovery Baseline Habitat Methodology and Overview

Baseline Scenario Habitat Methodology and Overview

Baseline Habitat Inputs

Habitat inputs for the Reorienting to Recovery baseline model run include current DSMhabitat values:

Fall Run Habitat

• DSMhabitat::fr_spawn

• DSMhabitat::fr_juv

• DSMhabitat::fr_fry

• DSMhabitat::fr_fp

Spring Run Habitat

• DSMhabitat::sr_spawn

• DSMhabitat::sr_juv

• DSMhabitat::sr_fry

• DSMhabitat::sr_fp

Winter Run Habitat

• DSMhabitat::wr_spawn

• DSMhabitat::wr_juv

• DSMhabitat::wr_fry

• DSMhabitat::wr_fp

Non Run Specific Habitat

• DSMhabitat::delta_habitat

Plus additional habitat acres from recently completed or in progress habitat restoration projects.

Project Catalog

The Reorienting to Recovery Planning team solicited input for the project catalog (via email, office hours, and one-on-one calls) from watershed associations, CDFW staff, DWR habitat workshop group and project proponents. They consolidated project lists received from CDFW and DWR into a Project Catalog of ~250 projects.

27 of the projects in the project catalog were identified for inclusion in the baseline based on the following criteria - at least one of the rulesets below must true:

• The project has greater that 50% funding allocated to it

• Environmental permitting for the project has been applied for and/ or granted

• The project is under construction

• The project or endeavor consists of a suite of management actions (e.g. re-operation of existing infrastructure) that are actively being considered by managers, have been approved, or are newly (within the last calendar year) being implemented

Project Catalog Summary

FlowWest summarized the project catalog by run, tributary, and habitat type to find total acres of habitat added to each Tributary. The following table shows summarized habitat added to each tributary:

Watershed	Habitat Type	Run	Proportion Suitable	Total Acres
Upper Sacramento River	spawning	fall	0.12	3.50
Upper Sacramento River	inchannel rearing	fall	0.10	12.10
Upper-mid Sacramento River	inchannel rearing	fall	0.78	1.95
Lower-mid Sacramento River	floodplain rearing	fall	0.90	114.00
American River	spawning	fall	0.12	13.00
American River	inchannel rearing	fall	0.78	2.00
American River	inchannel rearing	fall	0.10	1.00
American River	floodplain rearing	fall	0.90	2.00
Clear Creek	spawning	fall	0.12	9.50
North Delta	floodplain rearing	fall	0.90	5589.00
Paynes Creek	spawning	fall	0.12	3.00
Tuolumne River	inchannel rearing	fall	0.78	30.00
Tuolumne River	floodplain rearing	fall	0.90	90.00
Yuba River	floodplain rearing	fall	0.90	68.00
Cottonwood Creek	spawning	spring	0.12	1.00
Deer Creek	spawning	spring	0.12	35.33
North Delta	floodplain rearing	spring	0.90	5589.00
Lower-mid Sacramento River	floodplain rearing	spring	0.90	114.00
Tuolumne River	inchannel rearing	spring	0.78	30.00
Tuolumne River	floodplain rearing	spring	0.90	90.00
Upper Sacramento River	inchannel rearing	spring	0.78	7.00
Upper Sacramento River	spawning	spring	0.12	3.50
Upper-mid Sacramento River	inchannel rearing	spring	0.78	1.95
Yuba River	floodplain rearing	spring	0.90	68.00
North Delta	floodplain rearing	winter	0.90	5589.00
Lower-mid Sacramento River	floodplain rearing	winter	0.90	114.00
Upper Sacramento River	inchannel rearing	winter	0.78	199.88
Upper Sacramento River	spawning	winter	0.12	190.28
Upper-mid Sacramento River	inchannel rearing	winter	0.78	1.95

Methodology for integrating habitat projects into model SIT DSM inputs

The first step was to convert total project acres into usable area given the following assumptions:

• Floodplain use 90% suitable

• In channel suitability depends on gradient (Stillwater Sciences. 2012)

  Gradient	Percent Suitable
  < 0.04%	0.1
  0 - 2	0.78
  2 - 4	0.585
  4 - 8	0.195

• Spawning use 12% suitable

Habitat values for projects were not given for specific flows. To combine project acres with existing habitat we used a scaling approach (figure 1).

1) Calculate flow point of reference

We generated two helper functions to calculate flow reference points for adding inchannel and floodplain habitat.

Inchannel Point of Reference

For inchannel habitat we use the median flow over the entire modeled period 1980 - 2000. Flow inputs come from CalSim II benchmark from the 2019 Itp and 2020 BiOp. existing_cfs_median_comparison_plot takes in habitat_type, watershed, species, and a calsim_version and returns the median flow.

Example: Median flow for American River fall run inchannel rearing

existing_cfs_median_comparison_point("inchannel rearing", "American River", 
                                     "fr", 'biop_itp_2018_2019')
#> [1] 2640.5

Floodplain Point of Reference

For floodplain habitat we use the 2 year 30 day exceedence value.

existing_cfs_median_comparison_point("floodplain rearing", "American River", 
                                     "fr", 'biop_itp_2018_2019')
#> [1] 2433.429

2) Calculation proportion increase of habitat at flow point of reference

hab_prop_change_from_projects("inchannel rearing", "American River", 
                              "fr", "juv", "biop_itp_2018_2019")
#> Rows: 29 Columns: 6
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (4): watershed, habitat_type, run, gradient_class
#> dbl (2): total_acres, percent_suitable
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> `summarise()` has grouped output by 'watershed', 'habitat_type'. You can override using the `.groups` argument.
#> [1] 0.01211999

3) Scale existing habitat up by proportion increase

add_project_habitat <- DSMhabitat::fr_juv$biop_itp_2018_2019["American River" , , ] * 
  hab_prop_change_from_projects("inchannel rearing", "American River", "fr", "juv", "biop_itp_2018_2019")
#> Rows: 29 Columns: 6
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (4): watershed, habitat_type, run, gradient_class
#> dbl (2): total_acres, percent_suitable
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> `summarise()` has grouped output by 'watershed', 'habitat_type'. You can override using the `.groups` argument.

updated_habitat <- DSMhabitat::fr_juv$biop_itp_2018_2019["American River", , ] + add_project_habitat

Baseline Habitat Plots

Spawning Habitat

Below are spawning plots displaying spawning habitat changes from CVPIA SIT habitat (blue) to baseline (red) for each run.

Fall Run

Spring Run

Winter Run

Inchannel Rearing Fry Habitat

Below are inchannel fry rearing plots displaying rearing habitat changes from CVPIA SIT habitat (blue) to baseline (red) for each run.

Fall Run

Spring Run

Winter Run

Inchannel Rearing Juvenile Habitat

Below are inchannel juv rearing plots displaying inchannel rearing habitat changes from CVPIA SIT habitat (blue) to baseline (red) for each run.

Fall Run

Spring Run

Winter Run

Floodplain Rearing Habitat

Below are floodplain rearing plots displaying floodplain rearing habitat changes from CVPIA SIT habitat (blue) to baseline (red) for each run.

Fall Run

Spring Run

Winter Run

Delta Habitat (all runs)

Below is a delta-rearing habitat plot displaying delta-rearing habitat changes from CVPIA SIT habitat (blue) to baseline (red) for each run.