Attachment A 

To 

Resolution No. R5-2010-0046 

Basin Plan Amendments 

The Water Quality Control Plan for the Sacramento River and San Joaquin River 

Basins is amended as presented below. Deletions are indicated as strikethrough 

text (deleted text) and shaded fields (deleted field). Additions are shown as 

underlined text (added text). Italicized text (notation text) is included to locate 

where the modifications will be made in the Basin Plan. All other text changes 

are shown accurately, however, formatting on the page may change. 

Under the Chapter IV heading: “Regional Water Board Prohibitions, Item 6 on 

page IV-26.00, make the following changes: 

b. The discharge of agricultural subsurface drainage water to Salt Slough 

and wetland water supply channels identified in Appendix 40 is prohibited 

after 10 January 1997, unless water quality objectives for selenium are 

being met. This prohibition may be reconsidered if public or private 

interests prevent the implementation of a separate conveyance facility for 

agricultural subsurface drainage.

c. The discharge of agricultural subsurface drainage water to Mud Slough 

(north) and the San Joaquin River from Sack Dam to the mouth of the 

Merced River Mud Slough (north) is prohibited after 1 October 2010 

unless water quality objectives for selenium are being met. The discharge 

of agricultural subsurface drainage water to Mud Slough (north) and the 

San Joaquin River from the Mud Slough confluence to the Merced River is 

prohibited after 31 December 2019 unless water quality objectives for 

selenium are being met. This prohibition may be reconsidered if public or 

private interests prevent the implementation of a separate conveyance 

facility for agricultural subsurface drainage to the San Joaquin River. The 

prohibition becomes effective immediately upon Board determination that 

timely and adequate mitigation, as outlined in the 2010-2019 Agreement 

for Continued Use of the San Luis Drain1 has not been provided.

Under the Chapter IV heading: “Agricultural Drainage Discharges in the San 

Joaquin River Basin” page IV-31.00, make the following changes: 

Per the amendment to the Basin Plan for San Joaquin River subsurface 

agricultural drainage, approved by the State Water Board in Resolution No. 

 

1

 United States Department of the Interior, Bureau of Reclamation, Central Valley Project, 

California and San Luis & Delta-Mendota Water Authority, Los Banos, CA, Agreement for 

Continued Use of the San Luis Drain for the period January 1 2010, through December 31, 2019.
Attachment A to -2- 

Resolution No. R5-2010-0046 

96-078, as amended by Resolution No. R5-2010-0046 and incorporated 

herein, the following actions will be implemented. 

1. In developing control actions for selenium, the Regional Board will utilize a 

priority system which focuses on a combination of sensitivity of the beneficial 

use to selenium and the environmental benefit expected from the action. 

2. Control actions which result in selenium load reduction are most effective in 

meeting water quality objectives. 

3. With the uncertainty in the effectiveness of each control action, the 

regulatory program will be conducted as a series of short-term actions that 

are designed to meet long-term water quality objectives. 

4. Best management practices, such as water conservation measures, are 

applicable to the control of agricultural subsurface drainage. 

5. Performance goals will be used to measure progress toward achievement 

of water quality objectives for selenium. Prohibitions of discharge and waste 

discharge requirements will be used to control agricultural subsurface 

drainage discharges containing selenium. Compliance with performance 

goals and water quality objectives for nonpoint sources will occur no later 

than the dates specified in Table IV-4 for Mud Slough (north) and the San 

Joaquin River from the Mud Slough confluence to the Merced River.

6. Waste discharge requirements will be used to control agricultural 

subsurface drainage discharges containing selenium and may be used to 

control discharges containing other toxic trace elements. 

7. Selenium load reduction requirements will be incorporated into waste 

discharge requirements as effluent limits as necessary to ensure that the 

selenium water quality objectives in the San Joaquin River downstream of the 

Merced River inflow is achieved. The Board intends to implement adopted a 

TMDL for selenium in the San Joaquin River in 2001 after public review. 

---Additional changes are shown on the next page--- 
Attachment A to -3- 

Resolution No. R5-2010-0046 

Table IV-4. Compliance Time Schedule for Meeting the 4-day Average and 

Monthly Mean Water Quality Objective for Selenium 

Selenium Water Quality Objectives (in bold) and Performance Goals (in italics) 

1 The water year classification will be established using the best available estimate of the 60-20-20 San 

Joaquin Valley water year hydrologic classification (as defined in Footnote 17 for Table 3 in the State 

Water Resources Control Board’s Water Quality Control Plan for the San Francisco Bay/Sacramento-San 

Joaquin Delta Estuary, May 1995) at the 75% exceedance level using data from the Department of Water 

Resources Bulletin 120 series. The previous water year’s classification will apply until an estimate is made 

of the current water year.

Water 

Body/Water 

Year Type1

1 October

1996

1 October

2002

1 October

2005

1 October

2010

31 

December

2015

31 

December 

2019

Salt Slough and

Wetland Water

Supply Channels

listed in

Appendix 40

2 ug/L

monthly

mean

San Joaquin

River below the

Merced River;

Above Normal

and Wet Water

Year types 1

5 ug/L

monthly

mean

5 ug/L

4-day

avg.

San Joaquin

River below the

Merced River;

Critical, Dry,

and Below

Normal Water

Year types

8 ug/L

monthly

mean

5 ug/L

monthly

mean

5 ug/L

4-day

avg.

Mud Slough 

(north) and the 

San Joaquin 

River from Sack

Dam the Mud 

Slough

confluence to the 

Merced River

5 ug/L

4-day

avg.

15 ug/L

monthly 

mean

5 ug/L

4-day

avg.