Periodic Review of the 1995 Water Quality Control Plan for the San Francisco Bay/Sacramento-San

Joaquin Delta Estuary

Comments of

The Bay Institute

on

Vernalis Flow ObjectiveFebruary-April 14 and May 16-June 30

March 21, 2005

0

5000

10000

15000

20000

25000

0

10000

20000

30000

40000

50000

Flo

w (

cfs)

05000

10000150002000025000

05000

1000015000200002500030000

WY 2004Dry

WY 2003Below Normal

WY 2002Dry

WY 2001Dry

O N D J F M A M J J A S

Unimpaired

Actual

0

10000

20000

30000

40000WY 2000

Above Normal

San Joaquin River flows at Vernalis are subject to

greatest alteration during

ecologically critical February-

June period

Actual Vernalis flows as % of unimpaired:

2004: 23.5%

2003: 17.7%

2002: 19.9%

2001: 31.2%

2000: 38.5%

0

5000

10000

15000

20000

25000

0

10000

20000

30000

40000

50000

Flo

w (

cfs)

05000

10000150002000025000

05000

1000015000200002500030000

WY 2004Dry

WY 2003Below Normal

WY 2002Dry

WY 2001Dry

O N D J F M A M J J A S

Unimpaired

Actual

0

10000

20000

30000

40000WY 2000

Above Normal

SJ flow at Vernalis as % of unimpaired and total Delta inflow

1930 1940 1950 1960 1970 1980 1990 2000

Pe

rce

nt

(%)

0

5

10

15

20

25

30

35 SJ Basin runoff as % of total runoff

SJ basin flow (Vernalis) as % of total Delta inflow

SJ unimpaired as % of total unimpaired:no signif change over time, 1930-2004 average = 22.8%

SJ actual (Vernalis) as % of actual total Delta inflow:Significant decline over time (p<0.05)1930-2004 av. = 12.6%1996-2004 av = 11.7%2002-2004 av = 7.2%

1930 1940 1950 1960 1970 1980 1990 2000

Pe

rce

nt

(%)

0

5

10

15

20

25

30

35 SJ Basin runoff as % of total runoff

SJ basin flow (Vernalis) as % of total Delta inflow

Relative contribution of San Joaquin Basin to Delta inflow has declined

SJ flow at Vernalis as % of unimpaired and total Delta inflow

1930 1940 1950 1960 1970 1980 1990 2000

Pe

rce

nt

(%)

0

5

10

15

20

25

30

35 SJ Basin runoff as % of total runoff

SJ basin flow (Vernalis) as % of total Delta inflow

SJ unimpaired as % of total unimpaired:no signif change over time, 1930-2004 average = 22.8%

SJ actual (Vernalis) as % of actual total Delta inflow:Significant decline over time (p<0.05)1930-2004 av. = 12.6%1996-2004 av = 11.7%2002-2004 av = 7.2%

1930 1940 1950 1960 1970 1980 1990 2000

Pe

rce

nt

(%)

0

5

10

15

20

25

30

35 SJ Basin runoff as % of total runoff

SJ basin flow (Vernalis) as % of total Delta inflow

2003: 6.4%2004: 6.2%

Relative contribution of San Joaquin Basin to Delta inflow has declined

San Joaquin Basin Fall-run Chinook SalmonStanislaus, Tuolumne, and Merced Rivers only

Esc

apem

ent

(# o

f fi

sh)

0

20000

40000

60000

80000NaturalHatchery1967-1991 averageDoubling goal

1950 1960 1970 1980 1990 2000

Ret

urn

Rat

io

"co

ho

rt r

epla

cem

ent

rate

"

0

2

4

6

8

10

12Return RatioReturn Ratio = 1(population stable)

RR > 1 population increaseRR < 1 population decline

San Joaquin Basin Chinook

salmon populations are below the 1967-

1991 average and declining

San Joaquin Basin Fall-run Chinook salmon

S a c r a m e n t o B a s i n W i n t e r - r u n C h i n o o k S a l m o n

1 9 5 0 1 9 6 0 1 9 7 0 1 9 8 0 1 9 9 0 2 0 0 0

Es

ca

pe

me

nt

(# o

f fi

sh)

0

2 0 0 0 0

4 0 0 0 0

6 0 0 0 0

8 0 0 0 0

1 0 0 0 0 0

1 2 0 0 0 0

S a c r a m e n t o B a s i n S p r i n g - r u n C h i n o o k S a l m o n

Es

ca

pe

men

t (#

of

fish

)

0

1 0 0 0 0

2 0 0 0 0

3 0 0 0 0

S a c r a m e n t o B a s i n F a l l - r u n C h i n o o k S a l m o n

1 9 5 0 1 9 6 0 1 9 7 0 1 9 8 0 1 9 9 0 2 0 0 0

Es

cap

em

ent

(# o

f fi

sh)

0

2 0 0 0 0 0

4 0 0 0 0 0

6 0 0 0 0 0

8 0 0 0 0 0 N a t u r a lH a t c h e r y1 9 6 7 - 1 9 9 1 a v e r a g eD o u b l i n g g o a l

Winter-run

Spring-run

Fall-run

Sacramento Basin Chinook Salmon

In contrast, Sacramento

Basin Chinook salmon

populations have stabilized

or increased

Favorable ocean conditions and

improvements in freshwater flow

and habitat

Vernalis Flow (March-June, average cfs)

0 10000 20000 30000R

etu

rn R

atio

0

2

4

6

8

10

12

Vernalis Flow (March-June, average cfs)

0 10000 20000 30000

Es

ca

pe

me

nt

(# o

f fi

sh

)

0

20000

40000

60000

80000Regression: Escapement = 6632 + 1.6(average spring flow, cfs)

n = 47, p<0.001, r2 = 0.475

2003 Return Ratio = 0.4Most juveniles emigrated in 2001

2004 Return Ratio = 0.5Most juveniles emigrated in 2002

San Joaquin Basin Chinook salmon population size is directly related to Vernalis

flows during the juvenile outmigration

Since 1995 WQCP implemented

Vernalis Flow (March-June, average cfs)

0 10000 20000 30000

Ret

urn

Rat

io

0

2

4

6

8

10

12

Vernalis Flow (March-June, average cfs)

0 10000 20000 30000

Es

ca

pe

me

nt

(# o

f fi

sh

)

0

20000

40000

60000

80000Regression: Escapement = 6632 + 1.6(average spring flow, cfs)

n = 47, p<0.001, r2 = 0.475

2003 Return Ratio = 0.4Most juveniles emigrated in 2001

2004 Return Ratio = 0.5Most juveniles emigrated in 2002

Since 1995 WQCP implemented

Population growth (return ratio) is also related to Vernalis flows during juvenile outmigration

1 -

Vernalis Flow (March-June, average cfs)

0 10000 20000 30000

Ret

urn

Rat

io

0

2

4

6

8

10

12

Vernalis Flow (March-June, average cfs)

0 10000 20000 30000

Es

ca

pe

me

nt

(# o

f fi

sh

)

0

20000

40000

60000

80000Regression: Escapement = 6632 + 1.6(average spring flow, cfs)

n = 47, p<0.001, r2 = 0.475

2003 Return Ratio = 0.4Most juveniles emigrated in 2001

2004 Return Ratio = 0.5Most juveniles emigrated in 2002

Since 1995 WQCP implemented

Population increase: 94% of years with flows >5000cfs

Population decrease: 60% of years with flows <5000 cfs

1 -

2D Graph 2

San Joaquin River flow:Export ratio(March-June)

0 1 2 3 5 10 15 20

Re

turn

Ra

tio

0

2

4

6

8

10

12

Ratio of Vernalis flows to Delta export rates also affects population growth (return ratio)

Since 1995 WQCP implemented

-1

2003 return ratio = 0.42004 return ratio = 0.5

2D Graph 2

San Joaquin River flow:Export ratio(March-June)

0 1 2 3 5 10 15 20

Re

turn

Ra

tio

0

2

4

6

8

10

12

Population increase: 95% of years with flow:export >1.0

Population decrease: 67% of years with flow:export <1.0

Since 1995 WQCP implemented

-1

2003 return ratio = 0.42004 return ratio = 0.5

Species or Run O N D J F M A M J J A S

Fall Chinook

Late fall Chinook

Winter Chinook

Spring Chinook

Steelhead

Delta smelt

31-day pulse flow not sufficient to protect anadromous and estuarine fishes

Migration of juvenile Chinook salmon and steelhead NOT restricted to April 15-May 16

1970 1975 1980 1985 1990 1995 2000 2005

Ve

rna

lis

flo

w:E

xp

ort

ra

tio

0

1

2

3

101520

April 15-May 15 (VAMP) March 15-April 14 May 16-June 15

Flow:export ratio conditions before and after the 31-day pulse flow are poor and worsening

Restricted migration period reduces genetic and phenotypic diversity

Region % of Fishes That Are Native Species

1967-2001

mean (±1 standard error)

South Delta 0.3% (±0.4)

Central Delta 10% (±2)

North Delta 29% (±3)

West Delta 49% (±4)

Inadequate Vernalis flows degrade estuarine habitat in the south and central Delta

Prevalence of non-native species is a well-documented indicator of degraded habitat

CDFG Fall Midwater Trawl Survey

Freyer and Healey (2003)

Sampled: March-November 1992-1999

• Only 24% of species and 0.5% of fish in south Delta were native species

• Fish species composition in south Delta related to flow

• Native fishes associated with higher flows

Vernalis: <1800 cfsExports: >7500 cfsSJR:Export ratio: 1:4 (0.24)

Freshwater inflows to south Delta are important to many estuarine fishes

Abu

ndan

ce In

dex

0

10

20

30

40

50

60

70

1960 1970 1980 1990 20000

300

600

900

1200

1500

Summer Townet Survey(juvenile delta smelt)

Fall Midwater Trawl Survey(subadult & adult delta smelt)

Abu

ndan

ce In

dex

Delta smelt population

has declined to record low

levels

Recommendation

SWRCB should revise the Bay-Delta Plan to adopt more protective Vernalis flow objectives for the February-April 14 and May 16-June period.

Monthly Vernalis objectives should be based on criteria relating to hydrology, San Joaquin Basin contributions to Delta inflow, and fish and estuarine habitat needs.

Vernalis flows should be:

1. Based on annual and monthly hydrology2. Based on relative contribution of San Joaquin

Basin to Delta inflow (>20% of total minimum require Delta inflow in BN, D and C years; >10% of actual Delta inflow in W, AN, and BN years)

3. >5000 cfs for three consecutive months in W and AN years, >5000 cfs for two consecutive months in BN years

4. >1500 cfs in all months, all years5. <7000 cfs to allow installation of the Head of Old

River Barrier6. Linked to export rates to achieve March-June

Vernalis:export ratio >1.0

Month Water Year Type

W AN BN D C

Feb 3420 3420 2280 2280 1500

March 5000 5000 3420 2280 1500

April 1-14 7000 5000 5000 5000 2000

April 15-May 15

31-day flow objective as determined by VAMP experimental design

May 16-31 7000 5000 5000 3420 2000

June 5000 5000 3420 2280 1500

Proposed Vernalis flows (monthly average) February-April 14, May 16-June

0

5000

10000

15000

20000

25000

0

10000

20000

30000

40000

50000

Flo

w (

cfs)

05000

10000150002000025000

05000

1000015000200002500030000

WY 2004Dry

WY 2003Below Normal

WY 2002Dry

WY 2001Dry

O N D J F M A M J J A S

Unimpaired

Actual

0

10000

20000

30000

40000WY 2000

Above Normal

Proposed Vernalis flows

for Water Years 2000-2004

0

5000

10000

15000

20000

25000

0

10000

20000

30000

40000

50000

Flo

w (

cfs)

05000

10000150002000025000

05000

1000015000200002500030000

WY 2004Dry

WY 2003Below Normal

WY 2002Dry

WY 2001Dry

O N D J F M A M J J A S

Unimpaired

Actual

0

10000

20000

30000

40000WY 2000

Above Normal

2004: 108 TAF27% (v 24%) of unimpaired

2003: 357 TAF27% (v 18%)

2002: 204 TAF26% (v 20%)

2001: 54 TAF33% (v 31%)

2000: 0 TAF38% (v 38%)