Technical Analysis of In-Valley Drainage Management 

Strategies for the Western San Joaquin Valley, California 

Open File Report 2008—1210 

U.S. Department of the Interior 

U.S. Geological Survey

 
ii

Cover Photo: San Joaquin-Sacramento River Delta, California, NASA, 2006 

 
iii

Technical Analysis of In-Valley Drainage Management 

Strategies for the Western San Joaquin Valley, California 

By Theresa S. Presser and Steven E. Schwarzbach

Open File Report 2008—1210 

U.S. Department of the Interior 

U.S. Geological Survey 

 
iv

U.S. Department of the Interior 

DIRK KEMPTHORNE, Secretary 

U.S. Geological Survey 

Mark D. Myers, Director 

U.S. Geological Survey, Reston, Virginia 2008 

For more information on the USGS—the Federal source for science about the Earth, 

its natural and living resources, natural hazards, and the environment: 

World Wide Web: http://www.usgs.gov 

Telephone: 1-888-ASK-USGS 

Suggested citation: 

Presser, T. S., Schwarzbach, S. E., 2008, Technical Analysis of In-Valley Drainage Management Strategies for the 

Western San Joaquin Valley, California, U.S. Geological Survey, Open-File Report 2008-1210, 37 p.

[http://pubs.usgs.gov/of/2008/1210/].

Any use of trade, product, or firm names is for descriptive purposes only and does not imply 

endorsement by the U.S. Government. 

Although this report is in the public domain, permission must be secured from the individual 

copyright owners to reproduce any copyrighted material contained within this report. 
v

Contents 

Executive Summary ....................................................................................................................................................... 1

Introduction .................................................................................................................................................................... 4

Technical Analysis ......................................................................................................................................................... 5

Background ................................................................................................................................................................ 5

Sustainability of Discharge: Build-Out of Drains ......................................................................................................... 6

Reduction in Applied Water: Land Retirement and Isolation of Selenium ................................................................. 9

Reduction in Applied Water: Source Control .............................................................................................................10

Hydrologic Balance: Regional Groundwater Extraction from the Semi-Confined Aquifer ..........................................12

Storage of Concentrated Drainage Water on Land Surface: Mass Balance of Salt and Selenium in Waste 

Streams ....................................................................................................................................................................13

Ecological Risk of Selenium: integration of habitat areas in scaled-up reuse areas and enhanced evaporation 

systems .....................................................................................................................................................................23

Drainage Treatment ..................................................................................................................................................25

Final disposition: disposal of bio-waste, storage of salts, and closure plans .............................................................26

Concluding Perspective ................................................................................................................................................28

References ................................................................................................................................................................30

Appendix A: Description of Drainage Management Alternatives and Plans ..................................................................33

SLU Plan proposed in USFWS Conceptual Monitoring, Compliance, and Adaptive Management 

Plan: 2/28/08 draft .....................................................................................................................................................34

SLU Plan proposed in USBR Handout #4, San Luis Unit Drainage Implementation Plan, dated 2/12/08. ................35

Appendix B: Decision Analysis Modeling ......................................................................................................................36

Figures 

Figure 1.Projection of drained area, selenium loads, and salt loads (i.e. drainage need) for 1 to 50 years for the 

Westlands Water District (SLDFRE Planning Alternatives Report, 2001). ..................................................................... 7

Figure 2.Projection of selenium and salt concentrations (i.e. drainage need) for 1 to 50 years for the Westlands Water 

District (SLDFRE Planning Alternatives Report, 2001). ................................................................................................. 8

Figure 3.Projection of drained area, selenium loads, and salt loads (i.e. drainage need), for 1 to 50 years for the 

Northerly San Luis Unit districts (SLDFRE Planning Alternatives Report, 2001). .......................................................... 8

Figure 4.Projection of selenium and salt concentrations (i.e. drainage need) for 1 to 50 years for the Northerly San 

Luis Unit districts (SLDFRE Planning Alternatives Report, 2001). ................................................................................. 9

Figure 5.Components of sequential waste-stream for recently proposed in-valley drainage 

management plan. ........................................................................................................................................................14

Figure 6. Selenium and salt mass balance for SLDFRE EIS in-valley alternative with current acres retired (combined 

Westlands Area and Northerly Area). ...........................................................................................................................16

Figure 7. Selenium and salt mass balance for SLDFRE EIS in-valley/groundwater quality land retirement alternative 

with 100,000 acres retired (combined Westlands Area and Northerly Area).................................................................16

Figure 8. Selenium and salt mass balance for SLDFRE EIS in-valley/water needs land retirement alternative with 

200,000 acres retired (combined Westlands Area and Northerly Area). .......................................................................17

Figure 9. Selenium and salt mass balance for SLDFRE EIS in-valley/drainage-impaired lands land retirement 

alternative with 300,000 acres retired (combined Westlands Area and Northerly Area). ..............................................17

Figure 10. Selenium and salt mass balance for recently proposed in-valley management plan with 100,000 acres 

retired (combined Westlands Area and Northerly Area). ..............................................................................................18

Figure 11.Selenium and salt mass balance for a variation of recently proposed in-valley management plan (combined 

Westlands Area and Northerly Area; Westlands Area at full capacity). ........................................................................18
vi

Figure 12. Selenium and salt mass balance for theoretical in-valley alternative with equal proportion of drainage 

stored in reuse as that processed through waste-stream to reverse osmosis, bio-treatment, and enhanced solar 

evaporation (combined Westlands Area and Northerly Area). ......................................................................................19

Tables 

Table 1. Simulations of drainage produced under different land retirement alternative. ................................................ 9

Table 2. Simulations of drainage produced under moderate recharge reduction. ........................................................11

Table 3. Simulations of drainage produced under maximum recharge reduction. ........................................................11

Table 4. Selenium (Se) mass balance for land retirement alternatives;. .......................................................................20

Table 5. Selenium (Se) mass balance for Land Retirement Alternatives: calculated storage. ....................................21

Table 6. Average egg selenium concentrations (μg/g, dry weight) for bird eggs collected in April, May, 

and June, 2003 from the Panoche Drainage District reuse area. .................................................................................23

Table 7. Range of egg selenium concentrations (μg/g, dry weight) for bird eggs collected from 2003 through 

2006 from the Panoche Drainage District reuse area. ..................................................................................................24

Table 8. Geometric mean egg selenium concentration (μg/g, dry weight) for bird eggs collected from 2003 

through 2006 from the Panoche Drainage District’s reuse area. ..................................................................................24
vii

Conversion Factors 

Inch/Pound to SI 

Multiply By To obtain

Area

acre 4,047 square meter (m2) 

acre 0.4047 hectare (ha) 

acre 0.4047 square hectometer (hm2

) 

acre 0.004047 square kilometer (km2

) 

square foot (ft2

) 929.0 square centimeter (cm2) 

square foot (ft2

) 0.09290 square meter (m2) 

square inch (in2

) 6.452 square centimeter (cm2) 

section (640 acres or 1 square mile) 259.0 square hectometer (hm2

) 

square mile (mi2

) 259.0 hectare (ha) 

square mile (mi2

) 2.590 square kilometer (km2) 

Volume

acre-foot (acre-ft) 1,233 cubic meter (m3) 

acre-foot (acre-ft) 0.001233 cubic hectometer (hm3) 

Flow rate

acre-foot per day (acre-ft/d) 0.01427 cubic meter per second (m3/s) 

acre-foot per year (acre-ft/yr) 1,233 cubic meter per year (m3/yr) 

acre-foot per year (acre-ft/yr) 0.001233 cubic hectometer per year 

(hm3

/yr) 
Technical Analysis of In-Valley Drainage Management 

Strategies for the Western San Joaquin Valley 

By Theresa S. Presser and Steven E. Schwarzbach

Executive Summary 

The western San Joaquin Valley is one of the most productive farming 

areas in the United States, but salt-buildup in soils and shallow groundwater 

aquifers threatens this area’s productivity. Elevated selenium concentrations 

in soils and groundwater complicate drainage management and salt disposal. 

In this document, we evaluate constraints on drainage management and 

implications of various approaches to management considered in: 

3⁄4 the San Luis Drainage Feature Re-Evaluation (SLDFRE) Environmental 

Impact Statement (EIS) (about 5,000 pages of documentation, including 

supporting technical reports and appendices); 

3⁄4 recent conceptual plans put forward by the San Luis Unit (SLU) 

contractors (i.e., the SLU Plans) (about 6 pages of documentation); 

3⁄4 approaches recommended by the San Joaquin Valley Drainage Program 

(SJVDP) (1990a); and 

3⁄4 other U.S. Geological Survey (USGS) models and analysis relevant to the 

western San Joaquin Valley. 

The alternatives developed in the SLDFRE EIS and other recently 

proposed drainage plans (refer to appendix A for details) differ from the 

strategies proposed by the San Joaquin Valley Drainage Program (1990a). 

The Bureau of Reclamation (USBR) in March 2007 signed a record of 

decision for an in-valley disposal option that would retire 194,000 acres of 

land, build 1,900 acres of evaporation ponds, and develop a treatment system 

to remove salt and selenium from drainwater. The recently proposed SLU 

Plans emphasize pumping drainage to the surface, storing approximately 33% 

in agricultural water re-use areas, treating selenium through biotechnology, 

enhancing the evaporation of water to concentrate salt, and identifying 

ultimate storage facilities for the remaining approximately 67% of waste 

selenium and salt. The treatment sequence of reuse, reverse osmosis, 

selenium bio-treatment, and enhanced solar evaporation is unprecedented and 

untested at the scale needed to meet plan requirements. 

All drainage management strategies that have been proposed seek to 

reduce the amount of drainage water produced. One approach is to reduce the 

amount of drainage per irrigated acre. From modeling simulations performed 

for the SLDFRE EIS of the Westlands Area of the SLU, theoretical minimums 

that can be achieved range from approximately 0.16 to 0.25 acre-feet per acre 

per year (AF/acre/year). Minimum production rates from the Northerly Area 
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

of the SLU are theorized as being much higher, approximately 0. 42 to 0.28 

AF/acre/year. Rates shown in the SLU Plans for drained acres from the two 

areas combined are 0.5 AF/acre/year at the subsurface drain stage and 0.37 

AF/acre/year after a series of on-farm and regional measures are instituted. 

Land retirement is a key strategy to reduce drainage because it can 

effectively reduce drainage to zero if all drainage-impaired lands are retired. 

Land retirement alternatives considered in the SLDFRE EIS differ for the two 

areas analyzed in the SLU. The Northerly Area is to retire a nominal 10,000 

acres and Westlands is to retire up to 300,000 acres. The initial land 

retirement option recently put forth in the SLU Plans predicted drainage 

volume reductions that are consistent with 200,000 acres of land retirement, 

but only 100,000 acres of land retirement was proposed. 

Within the proposed area of drainage there are, for all practical 

purposes, unlimited reservoirs of selenium and salt stored within the aquifers 

and soils of the valley and upslope in the Coast Ranges. Salt imported in 

irrigation water is estimated to be at least 1.5 million tons per year for the 

Westlands and Northerly Areas (SJVDIP, 1998). Analysis of the land 

retirement alternatives presented in the SLDFRE EIS indicates that land 

retirement of a minimum of only 100,000 acres results in the annual pumping 

to the surface of 20,142 pounds of selenium or about a million pounds of 

selenium over a 50 year period. Retiring 200,000 acres results in an annual 

pumping of 14,750 pounds of selenium; and retiring 300,000 acres reduces 

selenium pumped to the surface annually to 8,756 pounds, almost all of which 

is produced in the Northerly Area. 

A selenium mass balance analysis by USGS quantifies the amount of 

selenium, in general, exposed on the landscape and specifically contained in 

each waste-stream component (e.g., regional collector, reuse area, reverse 

osmosis facility, selenium bio-treatment plant, and enhanced solar evaporator 

system) for the SLDFRE EIS land retirement alternatives and recently 

proposed SLU Plans. A third of the selenium is lost in the first step at the 

agriculture water reuse areas. Selenium bio-treatment, if successful, would 

remove another 66% of the selenium from the waste stream, leaving a wastestream of 10 μg/L to be evaporated. Salt produced and stored at the surface in 

solar evaporators in the 100,000-acre, 200,000-acre and 300,000-acre 

alternatives totals 412,000, 307,000 and 181,000 tons per year. At 50 years, 

the 100,000-acre land retirement option will require salt storage of 20 million 

tons in these evaporators or landfills. This salt will be contaminated with a 

variety of trace elements common in drainage waters including selenium, 

boron, molybdenum, chromium, and arsenic. 

 Storage of salts in the aquifer below irrigated lands will also occur. 

Useable groundwater may be defined by the amount of total dissolved solids it 

contains. Regardless of what drainage plan is implemented, the amount of salt 

in groundwater will increase. Based on projections of future total dissolved 

solids in groundwater of the Westland and Northerly Areas, the useable life of 

the aquifer under various irrigation and drainage management goals is 

estimated to be between 25 and 220 years. 

2
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

The hydrologic imbalance in the western San Joaquin Valley can be 

partly addressed through a program that substitutes groundwater pumping for 

surface water delivery, thus helping to shift the groundwater budget from 

large surplus to small deficit and to stem any expansion of the drainage 

problem through time with continued irrigation. USGS models estimate that if 

pumped ground water is substituted for surface water deliveries there are 

several significant benefits: (1) the water table will be lowered under existing 

impaired lands; (2) the future area of land impacted by bare soil evaporation 

will be reduced; (3) up to 400,000 acre feet of surface water deliveries will be 

offset by groundwater pumping of about 320,000 AF/year and 80,000 AF/year 

by improvements in ground-water efficiency; and (4) the amount of 

drainwater that would need to be brought to the surface and treated will be 

reduced, thus reducing both cost and potential ecological risk. Coupling this 

type of ground-water flow model with salt and selenium biogeochemical 

models would yield an integrated approach to predicting water, salt, and 

selenium transport and identifying any potential degradation of aquifer 

resources that might accompany such a regional program. 

Given the amount of analysis and documentation available from the 

SJVDP and recent re-evaluations of drainage management, the USGS 

identifies not a lack of information, but rather a lack of decision analysis tools 

to enable meeting the combined need of sustaining agriculture, providing 

drainage service, and minimizing impacts to the environment. A more formal 

decision-making process may better address uncertainties (e g., the scaling up 

of re-use areas and enhanced solar evaporators; the feasibility of bio-treatment 

of drainwater containing 32,500 mg/L salt); help optimize combinations of 

specific drainage management strategies; and document underlying data 

analysis for future use. The benefits of such a process of decision analysis 

(refer to appendix B for details) are that it provides the flexibility to move 

forward in the face of uncertainty. It does, however, require long-term 

collaboration among stakeholders and a commitment to formalized adaptive 

management. 

3
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

Introduction 

The primary goal for the western San Joaquin Valley under the recently proposed drainage 

management plan by the San Luis Contractors remains the same as that defined by the SJVDP: lower 

the near- surface water table in waterlogged, saline land areas to help sustain agriculture (SJVDP, 

1990a; USBR, 2008). Complicating that goal, however, is the complexity of managing selenium, a 

toxicant to fish and wildlife that is leached from agricultural lands (Presser and Ohlendorf, 1987). The 

Westlands Water District within the San Luis Unit of the Central Valley Project is potentially the 

greatest generator of selenium when compared to the more northerly and southerly areas because its 

lands encompass the Panoche Creek alluvial fan (Presser, 1994). This fan and inter-fan area receive 

the most seleniferous runoff and erosion from the Coast Ranges. 

The SJVDP (1990a) identified three planning alternatives to achieve sustained agriculture and 

address selenium: 

3⁄4 conservation and recycling of irrigation-agricultural water; 

3⁄4 retirement of irrigated land overlying areas of containing shallow ground water with elevated 

concentrations of selenium; 

3⁄4 extraction of irrigable water from deep within the semi-confined aquifer. 

In terms of selenium, isolating selenium in the aquifer was identified as beneficial in 

comparison to discharge to surface impoundments or the San Joaquin River. Mitigation for selenium 

would still be necessary, but the potential for saving water through improved source control would 

help offset adverse effects by providing additional wetlands. Land retirement could also create 

terrestrial habitat, but only up-gradient lands would be considered unaffected by selenium. 

The SJVDP (1990a) addressed identifying the mix of strategies with associated performance 

criteria (triggers) and contingency options that were needed to achieve a certain quantitative outcome 

(for example, see figure 28 in SJVDP, 1990a). The criterion most used in the SJVDP to measure 

progress was a reduction in drainage (i.e., a decrease in the amount of acre-feet of drainage produced 

per acre per year, AF/acre/year). A minimum amount of water is needed to achieve salt balance (i.e., 

some water must pass the root zone to leach salt and maintain soil productivity). However, the amount 

above that, called non-beneficial deep percolation, was considered to contribute to problem water. 

Thus, the potential for reduction in deep percolation and the amount of problem water produced can be 

used to compare and objectify current alternatives and proposals. Inherent in all drainage reduction 

alternatives is a reduction in applied water (i.e., water retirement) because drainflow is directly 

proportional to shallow groundwater table levels. Feasibility of implementing options also depended 

on compensating benefits in the form of reduced costs of handling drainage regionally and in 

economic return to landowners from the sale and lease of the water supply no longer needed for 

irrigation (SJVDP, 1990a). 

Alternatives for providing drainage service for the western San Joaquin Valley were recently 

re-evaluated (USBR, 2001; 2002; 2005) (refer to appendix A for detailed descriptions). These efforts 

culminated in a SLDFRE EIS in 2006 and a Record of Decision (ROD) for the project in 2007. Of the 

in-valley options shown in the SLDFRE EIS, land retirement of all drainage-impaired lands 

(Drainage-Impaired Area alternative) was demonstrated as the preferred alternative. Under this 

alternative, 300,000 acres of land would be retired in Westlands Water District and drainage 

production in that district would theoretically be reduced to zero. In the ROD, retiring 200,000 acres 

of land (the Water Needs alternative) was selected as the alternative to be implemented based on 

further considerations of State and local impacts to agriculture. This alternative would retire lands 

such that the water needs of the lands remaining in production could be met by the foreseeable water 

4
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

supply from the Central Valley Project (CVP) water contracts (assumed at 70%) held by the associated 

water districts and groundwater resources for the area. The retired acreage would include lands with 

selenium concentrations > 20 μg/L in the shallow ground water. A third land retirement alternative 

(the Groundwater Quality alternative) considered in the SLDFRE EIS was to retire all lands with 

selenium concentrations > 50 μg/L in the shallow ground water (i.e., approximately 100,000 acres). 

Although not explicitly stated, the option recently proposed by Westlands Water District is similar to 

the Water Needs alternative in terms of regional drainage produced, but acres of land to be retired is 

unclear. An estimate of 100,000 acres land retirement has been suggested, which would include lands 

retired under previous settlement agreements, but not lands specifically targeted to contain selenium as 

envisioned by the SJVDP. 

In recent negotiations, Westland Water District has proposed to assume the responsibility of 

drainage service using an array of drainage reduction, treatment, and disposal options, but not 

necessarily with land retirement as the primary driver (appendix A). Hence, as with the SJVDP, a mix 

of strategies is being proposed that depends on different elements of drainage reduction and that 

potentially could serve many needs (e.g., lowering the water table; agricultural suitability; selenium 

containment). Given here is a preliminary analysis to help understand, frame, and quantify various 

drainage management strategies. In addition to the SLDFRE EIS and supporting information for the 

recent proposal, our analysis is mainly based on USGS led investigations and collaborative program 

data [e.g., SJVDP, 1990a, b; San Joaquin Valley Drainage Implementation Program (SJVDIP), 1998; 

SJVDIP Land Retirement Committee Report, 1999; Presser, 1987; 1994; Belitz and Phillips, 1993; 

Brush et al., 2006; Presser and Luoma, 2006). Presser and Luoma (2006) recently compiled the 

drainage history of the San Joaquin Valley and documented current reservoirs of salt and selenium in 

order to understand and model selenium loads that potentially would be available if out-of-valley or 

in-valley disposal was again considered on a regional basis (see especially documentation of San 

Joaquin Valley loading scenarios and appendices A to D of Presser and Luoma, 2006). 

Technical Analysis 

Background 

In planning for an envisioned hydrologic balance for the valley, a distinction was made 

between managing the accumulated hydrologic imbalance (area of affected land) and managing the 

annual hydrologic imbalance (rate of water table rise) (SJVDP, 1990a; Presser and Luoma, 2006). 

Short-term objectives would work toward hydrologic balance by stemming the rate of deterioration, 

while reclaiming existing problem lands would require releasing from storage a large accumulation of 

water and salt. Achieving hydrologic balance would not achieve salt balance. Salts would continue to 

accumulate in the soils and aquifers of the San Joaquin Valley. Managed volume of drainage 

discharge would increase over a hypothesized 100-year planning period (USBR, 1978, 1983). Salt 

loads were calculated for a period of 50 years into the future, with a maximum release occurring after 

40 years of discharge. Later estimates (USBR, 1983), also planned for 100 years of discharge to an 

out-of-valley drainage canal, showed a slowing in the rate of increase after 40 years. 

A more recent evaluation in 1998 of salt importation showed a total annual imported salt of 1.5 

million tons per year to the western San Joaquin Valley (SJVDIP,1998). For the Westlands Water 

District alone, because there is no drainage outlet, the salt input was estimated at 453,000 tons of 

salt/year. The predicted conditions in the Westlands Water District showed the largest proportion of 

internal salt to imported salt for the five areas considered (CH2M HILL, 1988). Here, importation of 

higher quality water would have a diminished effect compared to other areas because of this large 

reservoir of salt. The Northern and Grassland areas showed high proportions of imported salt to 

5
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

internal salt and relatively low salt accumulations because of the availability of the San Joaquin River 

for salt discharge. 

In terms of assessing the build-up of selenium, calculation of the amounts of selenium stored in 

the soils and aquifers of the western San Joaquin Valley confirm that the nature of accumulation and 

potential release of selenium contaminated drainage is massive (Presser and Luoma, 2006). 

Calculations based on two scenarios show that no long-term reduction in selenium discharge would be 

expected for 63 to 304 years at the lower range of selenium reservoir projections and at an assumed 

selenium removal rate of 42,785 pounds (lbs) of selenium/year. A drainage alternative that exports 

wastewaters outside of the valley may slow the degradation of valley resources, but drainage alone 

cannot alleviate the selenium build-up in the valley, at least within a century, even if influx of 

selenium from the Coast Ranges could be curtailed. 

Selenium poses a hazard to fish and wildlife because of its reproductive toxicity at 

environmentally relevant concentrations and its tendency to accumulate in food chains (Skorupa, 

1998). The San Joaquin Valley provides critically important habitat for wintering waterfowl of the 

Pacific Flyway. Eight to twelve million ducks and geese, along with hundreds of thousands of 

shorebirds and other marsh birds annually winter or pass through the valley. The history of the 

ecological impacts of disposal of selenium at Kesterson National Wildlife Refuge within the valley is 

well documented (e.g., Presser and Ohlendorf, 1987; SJVDP, 1990a, b). Additionally from 1986 to 

1993, the National Irrigation Water-Quality Program (NIWQP) of the U.S. Department of the Interior 

(USDOI) studied whether contamination was induced by irrigation drainage in 26 areas of the western 

United States. This program developed guidelines to interpret effects on biota of selenium (USDOI, 

1998). These guidelines, along with revisions based on more recent studies and modeling, can be used 

to interpret and guide management and mitigation of the risk of selenium in food chains and wildlife. 

(Presser and Luoma, 2006). A recent proposed out-of-valley solution to extend the San Luis Drain to 

convey drainage from the valley to the San Francisco Bay-Delta was found to present substantial 

ecological risk due to selenium (SLDFRE EIS, 2006; Presser and Luoma, 2006). 

In terms of degradation of groundwater quality for irrigation, management of drainage as 

presented in the SJVDP again tended to enhance near-term (up to 50 years) protection of soils and offsite impacts of drainage discharges, while continuing to diminish the life of the westside aquifers for 

irrigation use. The SJVDP estimated under certain assumed conditions for the lands of the SLU that 

the remaining useful life of the semi-confined aquifer (usable groundwater containing less than 1250 

mg/L Total Dissolved Solids, TDS) was 25 to 150 years at a minimum and 65 to 220 years on average. 

Schoups et al. (2005) more recently used integrated soil chemistry and regional-scale hydrology 

modeling to show that sustainability of agriculture in the western San Joaquin Valley is threatened in 

two ways: (1) the storage of dissolved salt has increased continuously since 1945; and (2) deeper 

aquifers are accumulating salt, thereby degrading deep groundwater quality. 

Sustainability of Discharge: Build-Out of Drains 

The recent drainage management plan proposes to continue managing the annual imbalance, 

but also in the long-term proposes to start draining the accumulated salt and selenium from aquifers 

and soils of the San Joaquin Valley. In an initial projection of drainage need the projected drained 

acreage at the build-out of the project in 50 years is 225,000 acres for the Westlands Area and 35,600 

acres for the Northerly Area Area. (SLDFRE Preliminary Alternative Report, 2001, section 3). 

Nominal values of drainage volume (60,000 AF/year) and selenium concentration (50 μg/L) for the 

Westlands Area showed an average of 8,800 lbs selenium discharged per year at the build-out of the 

6
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

project at 50 years. Nominal values of drainage volume (10,500 AF/year) and selenium concentration 

(90 μg/L) for the Northerly Area showed an average of 2,500 lbs selenium discharge per year at the 

build-out of the project at 50 years. Although these values have been revised on a more specific basis 

(refer to later discussion, tables, and figures), the general scale of the proposed project and the trend of 

the analysis remain relevant for the drainage areas. For Westlands Area, (a) acreage, volume, salt and 

selenium loads increase for 40 years and then may remain at those levels for perpetuity; (b) salt and 

selenium concentrations decrease for 20-30 years to constant concentrations and then may remain at 

those levels for perpetuity (figures 1 and 2). For the Northerly Area, (a) acreage remains constant; (b) 

volume and salt and selenium loads decrease for 20 years and then may remain at those levels for 

perpetuity; (b) salt and selenium concentrations decrease for 20 years to constant concentrations and 

then may remain at those levels for perpetuity (figures 3 and 4). Figures 1 to 4 also illustrate to some 

degree the incremental installation of subsurface drains. As soon as drainage service is available, the 

existing area in the north Westlands Area with drains would connect immediately. Within the first 10 

years, approximately 30% of drains would be installed, while the installation of the remaining 70% 

would proceed over the next 40 years as a linear increase. In the Northerly Area, a linear increase is 

assumed. Drains would not discharge to the reuse facilities until construction of disposal facilities 

were within two years of completion. 

0

1

2

3

4

5

0

50

100

150

200

250

0 10 20 30 40 50

Westlands Water District

Build-Out

I

F

D

tons Se/year

tons salt/year X 100,000

drained acres X 1,000

years of proposed project

drained acres X 1000

tons salt X 100,000

tons selenium

acres

selenium

salt

8,800 lbs Se/year

(or 4.4 tons Se/year)

225,000 acres

330,000 tons

salt/year

SLDFRE PAR 2001, Section 3, Projection of Drainage Need

Figure 1. Projection of drained area, selenium loads, and salt loads (i.e. drainage need) for 1 to 50 years for the 

Westlands Water District (SLDFRE Planning Alternatives Report, 2001). 

7
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

0

50

100

150

200

250

0

30

60

90

120

150

0 10 20 30 40 50

Westlands Water District

0.3 AF/acre

S

T

selenium concentration, ppb Se

TDS concentration, ppm salt X 100

years of proposed project

3,600 ppm TDS

or salt

Se concentration (ppm Se)

TDS concentration X 100 (ppm salt)

50 ppb Se

at 50 year build-out

at 50 year build-out

if 0.5 AF/acre

then 30 ppb Se

SLDFRE PAR 2001, Section 3, Projection of Drainage Need and 2,160 ppm TDS

Figure 2. Projection of selenium and salt concentrations (i.e. drainage need) for 1 to 50 years for the Westlands 

Water District (SLDFRE Planning Alternatives Report, 2001). 

0

0.5

1

1.5

2

2.5

0

1

2

3

4

5

0 10 20 30 40 50

Northerly SLU Districts

Build-Out

R

O

M

tons Se/year

tons salt/year X 100,000

drained acres X 1,000

years of proposed project

tons selenium

tons salt X 100,000

drained acres X 1000

35,600 acres

2,600 lbs Se/year (or 1.3 tons/year)

52,174 tons

salt/year

acres

selenium

salt

SLDFRE PAR 2001, Section 3, Projection of Drainage Need

Figure 3. Projection of drained area, selenium loads, and salt loads (i.e. drainage need), for 1 to 50 years for 

the Northerly San Luis Unit districts (SLDFRE Planning Alternatives Report, 2001). 

8
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

0

50

100

150

200

250

0

30

60

90

120

150

0 10 20 30 40 50 60

U

R

selenium concentration, ppb Se

TDS concentration, ppm salt X100

years of proposed project

TDS concentration X 100 (ppm salt)

Se concentration (ppm Se)

at 50 year build-out

3,600 ppm TDS

or salt

90 ppb Se

Northern SLU Districts

0.3 AF/acre

at 50 year build-out

if 0.5 AF/acre

then 50 ppb Se

SLDFRE PAR 2001, Section 3, Projection of Drainage Need and 2,160 ppm TDS

Figure 4. Projection of selenium and salt concentrations (i.e. drainage need) for 1 to 50 years for the Northerly 

San Luis Unit districts (SLDFRE Planning Alternatives Report, 2001). 

Reduction in Applied Water: Land Retirement and Isolation of Selenium 

When lands are retired, there is an overall reduction in water applied to a district. In general, 

less water applied as irrigation means less drainage produced, which in turn means less drainage 

requiring treatment and storage. Table 1 shows amounts of drainage reduction in terms of AF/year 

and AF/acre/year that can be expected given a decrease in the area of land irrigated (SLDFRE EIS, 

appendix C, simulated 2050 drainflow). The assumption used in the SLDFRE EIS analysis of land 

retirement for calculating drainage quantity was that the percentage of CVP water contract supply 

available was 59%. This percentage differs from the assumption in the water-needs alternative of five 

districts receiving an average of 70% of their existing CVP contact amounts. 

Table 1. Simulations of drainage produced under different land retirement alternative. 

Alternative 

(acres retired) 

Westlands 

(AF/yr) 

AF/acre/yr Northerly

(AF/yr) 

AF/acre/yr Combined 

(AF/yr) 

Current acres 40,562 0.24 41,800 0.55 82,362 

100,000 acres 34,811 0.25 41,800 0.55 76,611 

200,000 acres 18,035 0.26 40,840 0.53 58,875 

300,000 acres 0 0 37,960 0.47 37,960 

Data inputs: SLDFRE EIS, appendix C, simulated 2050 drainflow. 

The compilation in table 1 shows separate analyses for the Westlands Area and the Northerly 

Area. The majority of land retirement is in the Westlands Area, with only nominal retirement in the 

Northerly Area of 10,000 acres (i.e., Broadview Water District). The range of retired acreage 

considered in the Westlands Area is from approximately 50,000 acres to 300,000 acres (table 1). 

9
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

Irrigation ceases on retired lands and groundwater pumping and surface-water deliveries are 

discontinued. The pumping rate assumed to continue under actively irrigated lands is 175,000 

AF/year within Westlands Area, an amount equal to average private supply reported in Westlands 

Water District 2003 Water Needs Assessment. The analysis shows that the amount of drainflow 

decreases as the amount of acreage retired increases. The rate of drainflow per acre remains 

practically constant for each alternative at 0.25 AF/acre/year for the Westlands Area under 

progressively more land retirement. Comparing among options, associated drainflow decreases from 

40,562 AF/year to zero AF/year as ultimately all drainage-impaired lands in the Westlands Area are 

retired. However, several conditions may be inherent in the resultant zero drainflow, namely to 

achieve this result, a balance of reduced irrigation and land and groundwater pumping is required to 

not increase or transfer drainage problems. The percent reduction in drainflow is 14% with increasing 

retirement by 31,437 acres; 56% with increasing retirement by 127,859 acres; and 100% with 

increasing retirement by 241,097 acres. 

The retired acreage considered in the Northerly Area is 10,000 acres (table 1). Drainflow 

remains essentially constant at 40,000 AF/year. The conditions inherent in achieving this drainflow 

include shallow-water management, seepage reduction, and drainage recycling. The Northerly Area 

shows a rate of drainflow almost two-fold higher than that of the Westland Area (0.55 AF/acre/year). 

One of the original intents of land retirement as envisioned by the SJVDP was to isolate 

selenium (SJVDP, 1990a). Recommended criteria for land retirement of irrigated farmlands listed by 

the SJVDP included retiring lands with poor groundwater quality (> 50 μg/L selenium) and retiring 

large contiguous blocks of land. Lands overlying areas of shallow ground water with concentrations 

of selenium exceeding 200 μg/L were considered special candidates for retirement (i.e., “hotspots”). 

As irrigation was stopped, selenium was contained as the shallow groundwater table dropped beneath 

those lands. To some extent, instead of contributing to their contamination, the dewatered area 

beneath the retired lands would then become a sink to receive contaminated water from adjacent lands. 

The feasibility of this strategy depended on the existence of shallow groundwater areas in which 

concentrations of selenium are much greater than those of surrounding areas (see SJVDP, figure 23 for 

1990a assessment and SLDFRE Plan Formulation Report Addendum, figure 3-2 for current 

assessment of selenium concentrations in shallow groundwater). More recent modeling of land 

retirement strategies shows that not all needs (e.g., drainage reduction, agricultural suitability; creation 

of habitat) can be served by one strategy (SJVDIP, 1991; Purkey and Wallender, 2001). If the goal is 

to reduce drainage, then the strategy would be to retire down-gradient water-logged lands. If the goal 

is to create a sustainable integrated production/habitat system, then up-gradient land retirement 

emerges as the most logical strategy. Implementation of a successful land retirement program may 

require an approach that weighs independently the benefits of drainage reduction, selenium reduction, 

habitat creation, water acquisition and removal of lands that are no longer productive. Such an 

approach would also serve to identify target lands within each category that might not be considered 

for land retirement under a voluntary land retirement program. 

 

10
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

Reduction in Applied Water: Source Control 

Tables 2 and 3 show how improved irrigation efficiency would decrease drainflow (or 

designated here as a more generalized reduction in recharge) (SLDFRE EIS, appendix C, simulated 

2050 drainflow). 

Table 2. Simulations of drainage produced under moderate recharge reduction. 

Alternative 

(acres retired) 

Westlands 

(AF/yr) 

AF/acre/yr Northerly

(AF/yr) 

AF/acre/yr Combined (AF/yr)

Current acres 20,647 0.18 34,160 0.42 54,807 

100,000 acres 17,676 0.19 34,160 0.42 51,836 

200,000 acres 9,085 0.19 33,040 0.40 42,285 

300,000 acres 0 0 31,280 0.36 31,280 

Data inputs: SLDFRE EIS, appendix C, simulated 2050 drainflow. 

Table 3. Simulations of drainage produced under maximum recharge reduction. 

Alternative 

(acres retired) 

Westlands 

(AF/yr) 

AF/acre/yr Northerly

(AF/yr) 

AF/acre/yr Combined (AF/yr)

Current acres 13,067 0.16 26,520 0.29 39,587 

100,000 acres 11,038 0.16 26,520 0.29 37,558 

200,000 acres 5,422 0.16 26,040 0.28 31,462 

300,000 acres 0 0 24,600 0.25 24,600 

Data inputs: SLDFRE EIS, appendix C, simulated 2050 drainflow. 

Moderate recharge reduction as applied to current acres and under various land retirement 

alternatives means improvements in irrigation efficiency would decrease drainflow rates. Maximum 

recharge reduction as applied to current acres and under various land retirement alternatives means 

additional improvements in shallow groundwater management, regional recycling, and seepage 

reduction (i.e., lining water supply canals), would decrease drainflow rates. Modeling efforts in the 

SLDFRE EIS and supporting documents use various estimates of areas drained (i.e., to install 

subsurface drains or drain), but most assume that only two-thirds of the areas identified would have 

on-farm drainage systems and that arability can be maintained under this assumption. 

For the Westlands Area, comparison of alternatives in terms of instituting various levels of 

source control options (current, moderate or maximum) within a land retirement alternative shows 

drainflow decreases from 40,562 to 13,067 AF/year, with concomitant reduction in AF/tiled acre/year 

from 0.24 to 0.16. The percent reduction in drainflow is from 49% with moderate recharge reduction 

for a total reduction of 68% with a maximum recharge reduction. For the Northerly Area under the 

same sets of alternatives, drainflow decreases from 41,800 to 26,520 AF/year, with a concomitant 

reduction in AF/tiled acre/year from approximately 0.50 to 0.28. The percent reduction in drainflow is 

from 18% with moderate recharge reduction for a total reduction of 37% with a maximum recharge 

11
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

reduction. A combined analysis can be more directly compared to data given in recent proposals (refer 

to later discussion). Overall our analysis shows that much can be done with a program of 

comprehensive recharge reduction (i.e., in essence, the linking of land retirement, water retirement, 

on-farm source control, and groundwater pumping options). Retiring of all drainage impaired lands 

would eliminate the need for drainage service in the Westlands Area. However, drainage management 

facilities would still be required in the Northerly Area, where land retirement is limited to a nominal 

10,000 acres (i.e., Broadview Water District) immediately downslope from the border with Westlands 

Water District. 

Hydrologic Balance: Regional Groundwater Extraction from the Semi-Confined Aquifer 

From a regional perspective, the drainage problem in the western San Joaquin Valley can be 

seen as a consequence of a hydrologic imbalance: more water is being added to the system than is 

being removed. Consequently, the water table is rising and there is a need for drainage. This 

hydrologic imbalance can be partly addressed through a regional program that substitutes groundwater 

pumping for surface water delivery (SJVDP, 1990a: Belitz et al., 1993). Thus the need for water 

within a district could be reduced further by the amount of groundwater pumped on adjacent lands to 

manage ground water levels and achieve hydrologic balance. Groundwater extraction was a strategy 

that is in the mix of strategies recommended by the SJVDP. Groundwater flow models, both those 

originally developed by the SJVDP and newly developed models, are available for the Westlands and 

Northerly Areas to provide the basis for consideration of a groundwater pumping strategy on a 

regional scale (SJVDP, 1990a; Belitz et al., 1993; Belitz and and Phillips, 1995; Barlow et al., 1996; 

Brush et al., 2004; 2006). 

As noted in the SLDFRE EIS (appendix C), “Although drainwater reduction actions other than 

the ones selected have been proposed in the Westside Regional Drainage Plan and could be 

implemented to reduce drainage flows (e.g., shallow groundwater pumping), it was determined that 

they were either not cost effective compared to disposal facilities, or it was not reasonable to assume 

that they would be implemented due to the uncertainty regarding effectiveness of action. Shallow 

groundwater pumping shows promise for reducing drainflows. However, additional information is 

needed to demonstrate its practical feasibility, including the potential uses for the pumped 

groundwater.” Given these statements and the assumptions used in simulations of drainage produced 

under different land retirement alternatives for the SLDFRE EIS (tables 2 and 3), there is a need to 

further understand current and future effects of ground-water pumping program. Specifically, in the 

SLDFRE EIS, the base-case assumption was 175,000 AF/year of pumping under actively irrigated 

lands; and in the Groundwater Needs alternative, the water supply included local groundwater supplies 

of 185,000 AF/year. 

A more recent study evaluated the effect of groundwater pumping to achieve an optimization 

of productive lands with no abandonment due to waterlogging (Barlow et. al., 1996). Belitz and 

Phillips (1995) proposed a hydro-geologic approach as an alternative to agricultural drains. They also 

described the expanding problem of bare-soil evaporation (i.e., land typically underlain by a water 

table between 5 to 7 feet of land surface where water is close enough to the surface to evaporate) that a 

regional groundwater program could manage:...“maintenance of present practices results in a 

worsening of the situation: the total area subject to bare-soil evaporation increases from 224 mi2

 in 

1990 to 344 mi2 in 2040, and drain flow increases from 25,000 ac ft/yr to 28,000 ac ft/yr. Although 

land retirement results in elimination of bare-soil evaporation and drain flow in the areas retired, it 

has little to no effect in adjacent areas. In contrast, regional-scale changes in recharge and pumping 

are effective for regional management. The area subject to bare-soil evaporation can be reduced to 78 

mi2

, and drain flow to 8000 ac ft/yr if (1) recharge is reduced by 15% (26,000 ac ft/yr) in areas that 

12
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

currently use surface and groundwater (362 mi2); (2) recharge is reduced by 40% (28,000 ac ft/yr) in 

areas that currently use only surface water (137 mi2

); and (3) pumping rates are uniformly 

incremented by 0.5 ft/yr (160,000 ac ft/yr) in both areas. If these water budget changes were to be 

implemented in the study area, and in adjacent areas with similar hydrogeologic characteristics, then 

approximately 400,000 ac ft/yr of surface water would be made available. Thus a shift in the 

hydrologic budget in the central part of the western San Joaquin Valley improves the prospects for 

sustaining agriculture in the area, and could provide substantial water resources for other uses.” 

Storage of Concentrated Drainage Water on Land Surface: Mass Balance of Salt and Selenium in 

Waste Streams 

The SJVDP planned for eventual disposal, storage, or treatment of a limited amount of 

drainwater (SJVDP, 1990a). Drainage reuse areas were to reduce the volume of drainage requiring 

ultimate disposal by reusing it on progressively more salt-tolerant crops. The volume reduction would 

reduce disposal costs and treatment costs, if treatment became necessary. The volume of water was 

reduced by plant evapo-transpiration, with dissolved constituents becoming more concentrated and 

potentially easier to manage. Seepage to groundwater aquifers also would potentially reduce volume, 

but further contaminates specific aquifers. Drainage water captured in the tile drainage system under 

these lands would be collected and pumped into local distribution centers to become a source for 

irrigation of progressively more salt-tolerant crops. In terms of eventual storage, the SJVDP 

recommended some evaporation ponds in some areas that were to be highly managed to be bird free. 

Mitigation of evaporation ponds with clean habitat also was necessary. 

The recently proposed reuse areas present opportunities for wildlife use and selenium 

exposure. Potential use of regulating ponds to help control flow as a part of the engineered reuse 

system and ponding during flood events in the treatment areas also may create a potential wildlife 

exposure risk similar to those originally realized at Kesterson National Wildlife Refuge (Presser and 

Ohlendorf, 1987). Selenium toxicity concerns in these areas and habitats are considered below (refer 

to Ecological Risk of Selenium). 

Components of the sequential waste-stream for the in-valley alternatives in the SLDFRE EIS 

and for the current proposal are (figure 5): 

• drainwater collection and conveyance systems, including the Delta-Mendota Canal Drain; 

• reuse facilities 

• reuse pumping stations to convey drainwater to treatment facilities 

• reverse osmosis (RO) treatment facilities 

• selenium bio-treatment facilities; and 

• evaporation ponds in EIS planning or enhanced solar evaporators in recent planning. 

13
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

four facilities

12 acres Northerly

36 acres WWD in North, Central, South

four facilities: 

Northerly

WWD North, Central, South

Northerly: solar evaporation and dehumidifier (330 acres total)

WWD: enhanced solar evaporators (3 facilities of 110 acres each in WWD North, Central, and South)

12,500 acres (12-15 re-use areas @ 1000 acre each)

Subsurface regional collector system

Drainage

Re-use

Reverse osmosis

Bio-treatment

Evaporation

Landfill For bio-waste

In-place landfill Salt encapsulated or sold

Drainage service

Closed subsurface system

Facilities

Figure 5. Components of sequential waste-stream for recently proposed in-valley drainage management plan. 

The draining of accumulated reservoirs of salt and selenium stored in the soils and aquifers of 

the valley to surface impoundment may have large-scale implications for the future of the valley in 

terms of tradeoffs of contaminated groundwater aquifers (i.e., life of the aquifer for irrigation and 

drinking water use) for contaminated land-surfaces (i.e., creation of salt waste dumps and landfills for 

designated bio-treatment waste). A selenium mass balance analysis quantifies the amount of selenium, 

in general, exposed on the landscape, and specifically, contained in each waste-stream component 

(e.g., regional collector, reuse area, reverse osmosis facility, selenium bio-treatment plant, and 

enhanced solar evaporator system—figures 6 through 12). Data used in deriving the selenium mass 

balance are compiled from SLDFRE Draft EIS, 2005, appendix C, table C5; SLDFRE EIS, 2006, 

section 2, Table 2.13-1; SLDFRE Plan Formulation Report Addendum, 2004, page 4-29; USFWS 

Conceptual Monitoring, Compliance, and Adaptive Management Plan, 2/28/08 draft; USBR Handout 

#4, San Luis Unit Drainage Implementation Plan, 2/12/08. 

In the SLDFRE EIS alternatives and in the recently proposed plan, selenium concentrations in 

drainflow increase through each step until the selenium bio-treatment step, in which the selenium 

concentration in the evaporated brine is reduced to 10 μg/L. Alternatives in the SLDFRE EIS 

originally showed evaporation ponds (water-column selenium regulatory requirement of < 2 μg/L) as 

the final reduction and storage step, but recent proposals have eliminated evaporated ponds and 

substituted enhanced solar evaporation as the final waste-stream step. Although the amounts 

discharged at the end of the waste-stream are not affected by this decision, the recently stated goal of 

14
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

10 μg/L for the evaporated brine is not discussed in terms of regulatory requirements to protect 

wildlife and human health (e.g., from aerosol spray drift or airborne particulate salt and selenium 

associated with enhanced solar technology). Additionally, EIS planning shows some drainflow from 

the reuse areas going directly to the selenium bio-treatment facility, while other variations show only 

drainflow from RO going to the selenium bio-treatment facility. This evolution in planning is 

important to the feasibility of selenium bio-treatment because of the reduction in efficiency or nonperformance expected as salt concentrations increase (measured in this case as TDS, Total Dissolved 

Solids). Drainage from a re-use with a TDS of 4,000 to 8,000 mg/L is more easily treated than 

drainage from a RO facility with a predicted TDS of 32,520 mg/l TDS (refer to later discussion). 

The selenium bio-treatment also includes a chemical reduction step to change the oxidation 

state and bioavailability of selenium in the final waste product. The concern addressed by this 

additional step is that bio-treatment, while causing a decrease in the concentration of selenium, also 

may cause a change in the form of selenium to a more bioavailable organic form of selenium that 

raises the overall bioaccumlative potential of the waste stream (SLDRE EIS, 2007, appendix B). 

The stream of RO treated water produced would be available for other uses, but some waterquality issues (e.g., boron and mercury) remain for the product water. For example for planning for 

agricultural use of RO product water, it would be necessary to dilute the concentration of boron in the 

product water by up to 36-fold with CVP water to obtain a boron concentration that would not impair 

plant growth (SLDFRE EIS, 2007, Response to Comments). 

The mass balance analysis also helps in consideration of the magnitude of mitigation for 

potential adverse impacts due to contaminant build-up, exposure to concentrated drainage wastestreams, and exposure to potential aerial dispersion of liquids and particulates. In addition to 

dedicated mitigation, buffer zones to moderate contamination have been suggested. As in the SJVDP 

strategies, successful mitigation may depend on identifying a dedicated source of water for such offsets. 

For comparison to projected selenium loads given here, the historical annual discharge from 

the Westlands subarea via the San Luis Drain was 4,776 lbs selenium, with a total of 17,400 lbs 

selenium discharged to Kesterson National Wildlife Refuge over the history of San Luis Drain usage 

(January 1981 to September 1985). The cumulative 17,400 lbs selenium is termed as one kesterson 

(kst). The use of this unit provides perspective on the mass of selenium that was a hazard to wildlife 

when released directly to a wetland (Presser and Piper, 1998). 

Figures 6 to 12 show conceptual diagrams annotated with drainage volumes, selenium 

concentrations, and selenium loads for the sequence of steps in a drainage waste-stream. Tables 4 and 

5 show compiled data in tabular form for comparison amongst alternatives. These mass balance 

illustrations for the SLDFRE EIS land retirement alternatives and the recently proposed drainage 

management plans are conceptualized with solar sprinkler evaporators as the terminal technology to 

incorporate the latest concepts on storing and concentrating drainage and to facilitate comparison 

amongst alternatives. As noted before, the amounts discharged at the end of the waste-stream are not 

affected by this decision to substitute evaporators for ponds. 

15
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

ag reuse

area

reverse

osmosis

Se biotreatment

solar

sprinkler

evaporator

Land Retirement: current acres

output from collector

69,645 AF/year

120 ppb Se

22,732 lbs Se

22,732 lbs Se 15,508 lbs Se 15,335 lbs Se 150 lbs Se

0 lbs Se

to waste

7,224 lbs Se stored

15,185 lbs to waste landfill

150 lbs Se waste

output from reuse

21,116 acre-feet/year

270 ppb Se

15,508 lbs Se

output from biotreatment

5,500 acre-feet/year

10 ppb Se

150 lbs Se

output from RO

10,558 acre-feet/year

534 ppb Se

15,335 lbs Se

Surface contamination

Groundwater contamination

Surface contamination

Groundwater contamination

Surface contamination

Groundwater contamination

- 32%

- 1%

68%

- 67%

input

96,578 AF

subsurface 

drainage

(218,020 acres

w/tile drains;

0.44 AF/acre)

466,951 tons salt waste

219,742 tons salt stored

686,693 tons salt 466,951 tons salt 466,951 tons salt 466,951 tons salt

Figure 6. Selenium and salt mass balance for SLDFRE EIS in-valley alternative with current acres retired 

(combined Westlands Area and Northerly Area). 

ag reuse

area

reverse

osmosis

Se biotreatment

solar

sprinkler

evaporator

Land Retirement: 100,000 acres (approximately 92,592 acres)

(reflecting retirement of lands with shallow groundwater quality of >50 ppb Se)

output from collector

61,036 AF/year

120 ppb Se

19,922 lbs Se

19,922 lbs Se 13,335 lbs Se 13,556 lbs Se 150 lbs Se

0 lbs Se

to waste

6,586 lbs Se stored

13,406 lbs Se waste

150 lbs Se waste

output from reuse

18,158 acre-feet/year

270 ppb Se

13,335 lbs Se

output from biotreatment

5,500 acre-feet/year

10 ppb Se

150 lbs Se

output from RO

9,333 acre-feet/year

534 ppb Se

13,556 lbs Se

Surface contamination

Groundwater contamination

Surface contamination

Groundwater contamination

Surface contamination

Groundwater contamination

- 33%

- 1%

67%

- 66%

input

85,000 AF

subsurface 

drainage

(187,116 acres

w/tile drains;

0.45 AF/acre)

616,078 tons salt 412,772 tons salt 412,772 tons salt 412,772 tons salt

203,306 tons salt stored

412,772 tons salt waste

Figure 7. Selenium and salt mass balance for SLDFRE EIS in-valley/groundwater quality land retirement 

alternative with 100,000 acres retired (combined Westlands Area and Northerly Area). 

16
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

ag reuse

area

reverse

osmosis

Se biotreatment

solar

sprinkler

evaporator

Land Retirement: 200,000 acres (approximately 193,956 acres)

(reflecting retirement of lands with shallow groundwater quality of >50 ppb Se)

output from collector

45,287 AF/year

120 ppb Se

14,782 lbs Se

14,782 lbs Se 10,083lbs Se 10,081 lbs Se 105 lbs Se

0 lbs Se

to waste

4,699 lbs Se stored

9,976 lbs to waste landfill

105 lbs Se waste

output from reuse

13,730 acre-feet/year

270 ppb Se

10,083 lbs Se

output from biotreatment

3,850 acre-feet/year

10 ppb Se

105 lbs Se

output from RO

6,941 acre-feet/year

534 ppb Se

10,081 lbs Se

Surface contamination

Groundwater contamination

Surface contamination

Groundwater contamination

Surface contamination

Groundwater contamination

- 32%

- 1%

- 67%

68%

tsp, 5/9/08

input

62,807 AF

subsurface 

drainage

(122,833 acres

w/tile drains;

0.51 AF/acre)

144,462 tons salt stored

306,981 tons salt waste

451,443 tons salt 306,981 tons salt 306,981 tons salt 306,981 tons salt

Figure 8. Selenium and salt mass balance for SLDFRE EIS in-valley/water needs land retirement alternative 

with 200,000 acres retired (combined Westlands Area and Northerly Area). 

ag reuse

area

reverse

osmosis

Se biotreatment

solar

sprinkler

evaporator

Land Retirement: 300,000 acres (approximately 308,000 acres)

(all drainage impaired lands retired; Northerly only; zero drainage from WWD)

output from collector

26,830 AF/year

120 ppb Se

8,757 lbs Se

8,757 lbs Se 5,949 lbs Se 5,948 lbs Se 73 lbs Se

0 lbs Se

to waste

2,808 lbs Se stored

5,875 lbs Se waste

73 lbs Se waste

output from reuse

8,100 acre-feet/year

270 ppb Se

5,949 lbs Se

output from biotreatment

2,695 acre-feet/year

10 ppb Se

73 lbs Se

output from RO

4,095 acre-feet/year

534 ppb Se

5,948 lbs Se

Surface contamination

Groundwater contamination

Surface contamination

Groundwater contamination

Surface contamination

Groundwater contamination

- 32%

- 1%

- 67%

68%

tsp, 5/9/08

input

36,440 AF

subsurface 

drainage

(47,500 acres

w/tile drains;

0.77 AF/acre)

181,110 tons salt stored

85,228 tons salt stored

266,338 tons salt 181,110 tons salt 181,110 tons salt 181,110 tons salt

Figure 9. Selenium and salt mass balance for SLDFRE EIS in-valley/drainage-impaired lands land retirement 

alternative with 300,000 acres retired (combined Westlands Area and Northerly Area). 

17
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

ag reuse

area

reverse

osmosis

Se biotreatment

solar

sprinkler

evaporator

Land Retirement: 100,000 acres

output from collector

45,287 AF/year

120 ppb Se

14,782 lbs Se

14,782 lbs Se 10,083 lbs Se 9,971 lbs Se 150 lbs Se

112 lbs Se to waste

4,699 lbs Se stored

9,821 lbs Se to waste landfill

150 lbs Se to waste

output from reuse

13,730 acre-feet/year

270 ppb Se

10,083 lbs Se

output from biotreatment

5,500 acre-feet/year

10 ppb Se

150 lbs Se

output from RO

6,865 acre-feet/year

534 ppb Se

9,971 lbs Se

Surface contamination

Groundwater contamination

Surface contamination

Groundwater contamination

Surface contamination

Groundwater contamination

Surface contamination

Groundwater contamination

68%

-0.4%

-67%

-0.6%

-32%

input

63,000AF

subsurface 

drainage

tsp, 5/9/08

(122,833 acres

w/tile drains; 

0.51 AF/acre)

142,880 tons salt stored

303,620 tons salt waste

446,500 tons salt 303,620 tons salt 303,620 tons salt 303,620 tons salt

Figure 10. Selenium and salt mass balance for recently proposed in-valley management plan with 100,000 acres 

retired (combined Westlands Area and Northerly Area). 

ag reuse

area

reverse

osmosis

Se biotreatment

solar

sprinkler

evaporator

Land Retirement: ? Acres

output from collector

45,287 AF/year

120 ppb Se

14,782 lbs Se

14,782 lbs Se 10,083 lbs Se 9,971 lbs Se 150 lbs Se

4,699 lbs Se stored

9,821 lbs Se to waste

150 lbs Se to waste

output from reuse

13,730 acre-feet/year

270 ppb Se

10,083 lbs Se

output from biotreatment

5,500 acre-feet/year

10 ppb Se

150 lbs Se

output from RO

6,865 acre-feet/year

534 ppb Se

9,971 lbs Se

Surface contamination

Groundwater contamination

Surface contamination

Groundwater contamination

Surface contamination

Groundwater contamination

- 32%

- 0.6%

- 67%

68%

Figure 11

tsp, 5/9/08

(122,833 acres

w/tile drains;

0.51 AF acre)

input

62,807 AF

subsurface 

drainage

112 lbs Se to waste

Surface contamination

Groundwater contamination

-0.4%

142,880 tons salt stored

303,620 tons salt waste

446,500 tons salt 303,620 tons salt 303,620 tons salt 303,620 tons salt

Figure 11. Selenium and salt mass balance for a variation of recently proposed in-valley management plan 

(combined Westlands Area and Northerly Area; Westlands Area at full capacity). 

18
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

19

ag reuse

area

reverse

osmosis

Se biotreatment

solar

sprinkler

evaporator

Land Retirement: theoretical scenario

output from collector

63,000 AF/year

120 ppb Se

20,563 lbs Se

20,563 lbs Se 10,083 lbs Se 9,971 lbs 150 lbs

0 lbs Se

to waste

10,480 lbs stored

9,821 lbs Se to waste

150 lbs Se to waste

output from reuse

13,730 acre-feet/year

270 ppb Se

10,083 lbs Se

output from biotreatment

5,500 acre-feet/year

10 ppb Se

150 lbs Se

output from RO

6,865 acre-feet/year

534 ppb Se

9,971 lbs Se

Surface contamination

Groundwater contamination

Surface contamination

Groundwater contamination

Surface contamination

Groundwater contamination

- 51%

- 1%

49%

- 48%

316,012 tons salt stored

303,620 tons salt waste

619,632 tons salt 303,620 tons salt 303,620 tons salt 303,620 tons salt

Figure 12. Selenium and salt mass balance for theoretical in-valley alternative with equal proportion of drainage 

stored in reuse as that processed through waste-stream to reverse osmosis, bio-treatment, and enhanced 

solar evaporation (combined Westlands Area and Northerly Area). 
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

Table 4. Selenium (Se) mass balance for land retirement alternatives; data is per year; for 50 year project, multiple by 50. 

land 

retirement 

alternative 

planned 

retired 

acres/ 

nominal 

acres in 

scenarios 

subsurface 

drainage/ 

regional 

drainage 

input 

(AF/yr) 

regional 

drainage collector 

output/reuse input 

(AF/yr) 

planned 

(μg/L 

Se) 

calculated 

load (lbs 

Se/yr) 

reuse 

output/ 

RO input 

(AF/yr) 

planned 

(μg/L 

Se) 

calculated 

load (lbs 

Se/yr) 

RO 

output/ 

biotreatment 

input 

(AF/yr) 

planned 

(μg/L 

Se) 

calcul

load 

Se/y

Groundwater Quality 

92,592/ 100,000 

85,000 61,036 120 19,922 18,158 270 13,335 9,333 534 13,556 

Water Needs 193,956/ 

200,000 

62,807 45,287 120 14,782 13,730 270 10,083 6,941 534 10,081 

DrainageImpaired Lands 

308,000/ 300,000 

36,440 26,830 120 8,757 8,100 270 5,949 4,095 534 5,948 

Proposed in Monitoring Plan, 2/28/08 

100,000 63,000 ? 

45,287* 

120 14,782 13,730 270 10,083 6,865 534 9,971 

Proposed in USBR handout #4, 3/12/08 

? 62,807 ? 

45,287* 

120 14,782 13,730 270 10,083 6,865 534 9,971 

* assumed from above from Water Needs alternative. Data inputs: Drainwater Quantity and Quality, Appendix C, Draft SLDFR EIS, Ta

Features and Specifications, All Disposal Options, SLDFRE EIS, Section 2, Table 2.13-1; Drainage Quantity and Quality and Drainwate

SLDFRE PFR, 2004, Addendum, page 4-29; USFWS Monitoring Plan, 2/28/08, for proposed drainage management; USBR Handout #4, 
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

Table 5. Selenium (Se) mass balance for Land Retirement Alternatives: calculated storage. Data is per year; for 50-year proj

land retirement 

alternative 

planned 

retired 

acres/ 

nominal 

acres in 

scenarios 

regional drainage 

collector output/ 

re-use input 

(calculated lbs 

Se/yr) 

storage at 

reuse area 

(calculated lbs 

Se/yr) 

% lbs Se 

storage in 

reuse area 

reuse output/ 

RO input 

(calculated lbs 

Se/yr) 

% lbs Se 

in RO 

waste to 

landfill 

RO output/ 

biotreatment 

input (calculated 

lbs Se/yr) 

% 

bio

w

Groundwater Quality 

92,592/ 100,000 

19,922 6,586 33 13,335 0 13,556 66 

Water Needs 193,956/ 

200,000 

14,782 4,699 32 10,083 0 10,081 67 

DrainageImpaired Lands 

308,000/ 300,000 

8,757 2,808 32 5,949 0 5,948 67 

Proposed in Monitoring Plan, 2/28/08 

100,000 14,782 4,699 32 10,083 0.4 9,971 67 

Proposed in USBR handout #4, 3/12/08 

? 14,782 4,699 32 10,083 0.4 9,971 67 

Data inputs: same as those for table 4. 
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

Our analysis includes four land retirement alternatives (figures 6-9): In-Valley alternative 

(current retired acres); Groundwater Quality alternative (100,000 acres retired); Water Needs alternative 

(200,000 acres retired); and Drainage-Impaired Area alternative (300,000 acres retired). In these EISderived alternatives, the proportion of selenium stored on the surface to that stored in a dedicated 

landfill was assumed not to vary by alternative (i.e., a constant 33% to reuse and 67% to waste-stream). 

Figures 10-11 show recent proposed alternatives of land retirement. Figure 12 shows a theoretical 

alternative that varies the proportion of drainage to reuse and to waste-stream (essentially a 50:50 

proportion of stored in reuse areas to treatment and disposal). All representations and calculations 

presume successful treatment is accomplished, thus these figures depict the most favorable outcomes 

possible. Note also that in recent proposals versions, the amount of subsurface drainage produced 

(about 63,000 AF/year at the subsurface drain stage and 45,000 AF/year after a series of on-farm and 

regional measures are instituted) is similar to that shown for the Water Needs land retirement 

alternative, but the amount of land retirement varies from 200,000 acres to 100,000 acres or less (table 

4). 

The land retirement alternatives differ in the amount of selenium brought to the surface for 

treatment and storage. The initial volume of drainage shown is assumed to be reduced through on-farm 

activities such as shallow groundwater management, seepage reduction, and recycling. The output 

selenium concentration from the regional collector is planned to be 120 μg/L. For the Groundwater 

Quality alternative, the Water Needs alternative, and the recently proposed alternative, 14,782 lbs 

selenium/year enter the series of treatment steps based on planned volumes. For the Drainage-Impaired 

Area alternative, zero lbs selenium enter the system from the Westlands Area and 8,757 lbs 

selenium/year enter the system from the Northerly Area. Passage through the reuse area increases the 

selenium concentration approximately two-fold to 270 μg/L, as the waste-stream is further concentrated. 

Approximately 33% of the selenium mass (4,699 to 6,586 lbs selenium/year) remains at the reuse areas. 

RO treatment again increases the selenium concentration two-fold to 534 μg/L. Little selenium is lost to 

RO waste (less than 1% or approximately 100 lbs selenium/year) and the majority of selenium proceeds 

to bio-treatment. With bio-treatment, the selenium concentration is reduced approximately 50-fold to 

10 μg/L and 13,556 to 5,948 lbs selenium/year is collected as bio-waste for disposal in landfills or other 

alternative method of final disposition such as encapsulation in-place. Only 73-105 lbs selenium/year is 

treated to enhanced solar evaporation. Thus, the majority of selenium is in the bio-waste and not in the 

evaporated salt component if bio-treatment is successful. 

In terms of salt, 616,078 to 266,338 tons salt/year enter the waste-stream in the illustrated 

scenarios. Approximately 33% of the total salt mass (85,228 to 203,306 tons salt /year) remains at the 

reuse areas. The TDS concentration of the drainwater is 32,520 mg/L as it is discharged from the RO 

step and enters the selenium bio-treatment step. Approximately 67% of the salt remains to be 

evaporated by the enhanced solar evaporation systems (181,110 to 412,772 tons salt/year) (figures 6-

12). 

At the build-out of the project after 50 years, a cumulative total of 996,100 lbs selenium and 30.8 

million tons salt will be discharged under the Groundwater Quality alternative (approximately 100,000 

acres retired). Selenium stored in surface reuse areas is estimated at 329,300 lbs/50 years, with salt 

storage in surface reuse areas at 10.2 million tons/50 years. Selenium in bio-waste is estimated at 

670,300 lbs/50 years, with salt storage at final disposition to landfill at 20.6 million tons/50 years. The 

project is designed to be at maximum capacity after 50 years and discharge may continue at that rate 

into perpetuity given the massive nature of the reservoirs of salt and selenium available for discharge. 

22
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

Ecological Risk of Selenium: integration of habitat areas in scaled-up reuse areas and enhanced 

evaporation systems 

Reuse areas are a crucial part of the proposed management plan and would be areas where 

integration with terrestrial habitats would take place. Planned reuse areas for the EIS in-valley 

alternatives range from 7,500 to 19,000 acres. This would represent up to a 10-fold scale-up from the 

existing pilot project of 1,800 acres. Additional concern is for ponding and creation of transitory 

aquatic habitats contaminated with selenium in reuse areas as part of management actions for 

maintaining flow and during rainfall events. 

A summary of data from the Panoche Drainage District reuse area in 2004 includes selenium 

concentrations in bird eggs collected from an accidentally flooded pasture within the reuse area (table 

6). Here, concentrated agricultural drainage (60 to 200 μg/L selenium) is being managed to reduce the 

amount of selenium discharged to the San Joaquin River. The reuse area of 1,800 acres is eventually 

planned to encompass 4,000 acres. Over 42 species of birds have been found to use this drainwater 

reuse pilot area. The average selenium concentration in avocet and stilt eggs was 58 μg/g dry weight, 

which exceeds the threshold for substantive risk (high risk, >10 μg/g selenium) by approximately 6-

fold. A reduction of hatchability and deformities of bird embryos would likely occur at these 

concentrations (USDOI, 1998; Skorupa, 1998). This accidental flooding event illustrates how small 

ponds are very inviting to aquatic birds of the valley because of already limited habitat opportunities. 

The timing of appearance of food webs in the ponds and immediate nesting also illustrates the need for 

vigilance on the part of management for this type of habitat. Concern is also warranted because 

selenium concentrations in bird eggs from the majority of reference site sampled were also above the 

high risk threshold (table 6), suggesting a landscape effect larger than the reuse area as management and 

storage of concentrated drainwater takes place over several years. 

Table 6. Average egg selenium concentrations (μg/g, dry weight) for bird eggs collected in April, May, and June, 

2003 from the Panoche Drainage District reuse area (n = number of eggs). 

stilt Avocet (stilt and avocet) killdeer blackbird

Flooded Project 46.6 

(5) 

68.6 

(9) 

60.8 

(14) 

15.3 

(11) 

Rest-of-project 19.9 

(4) 

12.2 

(2) 

17.3 

(6) 

11.4 

(9) 

Rice Fields Reference 5.4 

(10) 

---- 

(0) 

5.4 

(10) 

4.1 

(9) 

Project Reference (excluding rice field 

data) 

25.3 

(6) 

10.6 

(4) 

18.4 

(10) 

4.4 

(11) 

Project (total) 33.2 

(9) 

40.4 

(11) 

47.7 

(20) 

13.4 

(20) 

6.1 

(20) 

Reference (total) 15.0 

(15) 

10.6 

(4) 

12.4 

(20) 

4.25 

(20) 

5.4 

(20) 

23
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

Table 7. Range of egg selenium concentrations (μg/g, dry weight) for bird eggs collected from 2003 through 2006 

from the Panoche Drainage District reuse area. 

species 2003 2004 2005 2006

killdeer 5.8-33.5 2.79-31.3 6.9-32.2 4.37-54.7 

recurvirostrids (avocets and stilts) 9.8-98.9 7.53-48.7 22.6-45.7 3.39-95.1 

red-winged blackbirds 4.5-11.0 4.79-7.26 N/A 5.54-15.9 

Table 8. Geometric mean egg selenium concentration (μg/g, dry weight) for bird eggs collected from 2003 through 

2006 from the Panoche Drainage District’s reuse area. 

species 2003 2004 2005 2006

killdeer 12.5 13.1 15.9 22.8 

recurvirostrids (avocets and stilts) 39.0 15.3 35.3 23.0 

red-winged blackbirds 5.9 6.0 N/A 8.8 

Data inputs: San Joaquin River Water Quality Improvement Project, Phase I Wildlife Monitoring Reports: Harvey and 

Associates, 2004 and 2006. Number in parentheses = number of eggs. 

A compilation of data from 2003 through 2006 (tables 7 and 8) shows ranges and geometric 

mean selenium concentrations in bird eggs collected from the Panoche Drainage District reuse area. 

Selenium concentrations in bird eggs were consistently above concentrations associated with selenium 

toxicity to embryos during those four years. Selenium concentrations in avocets and stilts in 2006 

exceeded 90 μg/g dry weight, higher than during the flooding event of 2003. A bird egg selenium 

concentration of 90 μg/g dry weight is 9-fold higher than the substantive risk threshold in bird eggs and 

deformed embryos would be expected. 

The Panoche Drainage District has recently instituted additional measures to reduce selenium 

exposure of birds including: 

• decreasing the attractiveness of drainage ditches by netting or enclosing drains; 

• hazing birds nesting near irrigation and drainage ditches; 

• planning for the contingency of flooded fields; and 

• providing 50-acres of mitigation habitat. 

Provision of mitigation habitat acreage with a dedicated water source would compensate for 

decreased nesting on re-use habitat. Evaluation would be necessary to see whether the amount of 

mitigation was appropriate or successful, and what mitigation ratio should be applied to future reuse 

areas. 

The enhanced solar evaporator systems would be used at conditions that yield evaporation rates 

>90% so that residual liquid spray is minimized to the point that ponding does not occur. However, 

ponding has occurred in the past at the pilot project solar evaporator basin at Red Rock Ranch. In 1996, 

enough ponding occurred within the solar evaporator to attract birds to nest. Nests were also found at 

the adjacent reuse area where halophytes were being irrigated with concentrated drainwater. Use of 

24
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

concentrated drainage resulted in geometric mean selenium concentrations in stilt eggs of 58 μg/g dry 

weight, with 56.7% of the stilt embryos deformed. This is the highest incidence of selenium-induced 

avian teratogenesis reported by any field study to date. Killdeer, a species of bird known to feed over a 

wider range, showed a 14% rate of deformity. The recently proposed enhanced solar evaporators are to 

receive water at a selenium concentration of 10 μg/L. However, at this concentration there still may be 

a potential for selenium risk to wildlife, if performance does not meet specific criteria. 

A buffer zone of approximately 600 feet was suggested to protect agricultural crops from redeposition of salt downwind from sprinklers. Selenium concentrations were not measured to determine 

or assess spray drift of salt or selenium that may affect wildlife or human health (California Department 

of Water Resources, 2005). Airborne particulates from salt waste piles may provide an additional 

pathway of exposure to plants, wildlife, and humans for selenium and other trace elements. 

Drainage Treatment 

Selenium removal from agricultural drainage from the western San Joaquin Valley is hampered 

by the large amounts of associated salt in any waste stream subjected to treatment. Extensive testing of 

technologies for removal of selenium from the water-column utilizing chemical and biological processes 

as part of the SJVDP achieved little operational success or cost-effectiveness (SJVDP, 1990c). 

Drainage treatment to remove selenium was not one of the strategies recommended by the SJDVP 

(1990a). In the Preface to the San Joaquin Valley Drainage Program final report (1990a), Edgar 

Imhoff, head of the program, wrote that “...hopes for a master drain and expectations of a 

technological breakthrough in drainage water treatment are the reasons that the drainage problem has 

grown to nearly 500,000 acres and is adversely affecting the environment.” 

A review of treatment technologies in 2004, evaluated the advantages and disadvantage of a 

number of technologies specifically tested on agricultural drainage waters from the valley. Some initial 

reduction of selenium concentration is possible (e.g., from 400 μg/L to 100 μg/L), but achieving levels 

low enough to meet regulatory requirements (2-5 μg/L) to protect the environment were found difficult 

and expensive. 

Technologies for treatment and disposal of waste products as planned in the SLDFRE EIS 

alternatives were tested on pilot-project scale. Pilot projects for drainage treatment using RO and biotreatment are located in: (1) the Westlands Water District in partnership with the California Department 

of Water Resources and Red Rock Ranch Incorporated; and (2) the Panoche Drainage District. 

Different RO treatment technologies are being tested with various pretreatment steps to separate detrital 

material and salts such as calcium sulfate from the drainwater to prevent clogging and improve recovery 

of product water (e.g., tubular nano-filtration membranes, addition of amendments, vibrating 

membranes). Bio-treatment technologies utilize bacteria that metabolize selenium. Granular charcoal 

and the development of a biological film to support bacterial reduction transform dissolved selenium to 

a solid form. Enhanced evaporation technologies are being tested at Red Rock Ranch, the original site 

for using natural solar evaporation and spray technology. 

Documentation for selenium bio-treatment in the SLDFRE EIS states that, “The pilot test has 

also encountered and identified numerous design and operational deficiencies that have impaired the 

performance of the bio-reactors during the first half of 2004. Selenium concentrations in the treated 

effluent during this period have been variable but generally range between 15 and 100 ppb.” As stated 

in the initial SLDFRE DEIS: “Subsequent treatment and disposal of reused drainwater is dependent 

upon the TDS concentrations. Biological treatment of drainwater may not be effective or economical at 

25
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

TDS concentrations above 20,000 mg/L.” Hence two disposal schemes were differentiated based on 

drainwater TDS concentration: <20,000 mg/L TDS through a sequence that includes biological 

treatment; and >20,000 mg/L TDS through a sequence that uses enhanced evaporation system and 

thermal desalinization (SLDFRE DEIS, Section 2). 

In the recent drainage management proposal, the planned TDS concentration of the drainwater is 

32,520 mg/L as it is discharged from the RO step and enters the selenium bio-treatment step. Data 

compilations (SLDFRE FEIS appendix B, attachment B-2) show that conductivity of the test waters for 

biological treatment ranges from 4,200 to approximately 15,000 μS/cm. If conductivity measurements 

are converted to TDS measurements (conductivity X 0.76 = TDS), the range of TDS in selenium biotreatment test water becomes 3,192 to 12,692 mg/L. Salinity for the Panoche Drainage District test 

waters for the selenium bio-treatment system ranged from 5,400 to 16,700 μg/L. Thus, these TDS 

concentrations are at least two-fold below that level predicted as output from an RO facility. The 

compilation also shows over a three-month period of operation using a test solution of approximately 

10,050 mg/L TDS, that the selenium concentration in the effluent increased from 1.6 μg/L to 200 μg/L 

(i.e., an approximate 125-fold drop in efficiency). This testing is at an almost 3-fold dilution of the TDS 

concentration planned for the RO effluent that is to be subjected to selenium bio-treatment. The matrix 

of chemicals in the drainwater used to test selenium bio-treament also is not described. Results were 

also variable in terms of discharging an effluent that is predominantly selenate as originally required in 

the SLDFRE EIS to meet environmental needs. As mentioned previously, selenite and organo-selenium 

would be more readily taken up in the environment than selenate (Skorupa, 1998; refer to previous 

discussion). In response to comments provided for the SLDFRE EIS, the USBR stated that a nationally 

recognized water treatment expert will conduct an independent review of the RO and selenium biotreatment pilot studies, data analyses, and design assumptions by 2006. 

In their original conception, solar evaporation basins would be small and serve each farm on its 

own specific scale. The planned enhanced evaporation technologies were tested at a pilot project solar 

evaporator basin of 0.23 acres located at Red Rock Ranch (California Department of Water Resources, 

2006), the original site for using natural solar evaporation and spray technology (named Integrated onFarm Drainage Management or IFDM). The proposed enhanced solar evaporators would cover an area 

of 330 acres in the Westland Area and the Northerly Area (six facilities of 110 acres each), a scale-up of 

approximately 1400-fold in both the Westlands Area and the Northerly Area. 

Final disposition: disposal of bio-waste, storage of salts, and closure plans 

Further tracking of the final disposition of salt and bio-waste to dedicated disposal areas would 

be necessary to complete the entire quantification and impact evaluation of the proposed waste-stream. 

The assumed combined flow rate to the bio-treatment facility in the recently proposed drainage 

management plan is approximately 6,850 AF/year. Bio-treatment modules are planned for treating 1000 

AF/year with shared flushing systems. The SLDFRE EIS states that the bio-treatment sludge will be 

disposed of in accordance with applicable regulations. Additionally, flushing decant water from various 

process steps would be disposed of in evaporation ponds or recycled back to the treatment plant 

(SLDFRE EIS, Appendix B). The more recent plan states that solid bio-waste will be disposed/reused 

appropriately. 

26
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

The concentration of selenium in liquids associated with the sludge bio-waste in the scenarios 

illustrated in figures 6-12 may be as high as 1,068 μg/L if a two-fold concentrating factor is assumed. 

The final concentration of selenium in the bio-waste would depend on an assumed density, but the 

potential exists for the production of liquids and solids that would be designated or hazardous selenium 

wastes. The selenium criteria for a hazardous waste are 1,000 μg/L for a liquid and 100 μg/g wet 

weight for a solid (U.S. Department of Health and Human Services, 1996). 

If 100,000 acres of land is retired under the Groundwater Quality alternative, then 412,772 tons 

salt/year are available for storage at the end of the evaporation process. Assuming a bulk dry density of 

1 g/cm3

, then 13.24 million feet3 salt are produced per year. At one-foot depth, this amount would cover 

311 acres. In 50 years, the salt waste pile would rise to 50 ft on the assumed 311 acres. This amount 

would be produced each 50 years into perpetuity. 

As noted before, airborne particulates from salt waste piles may provide an additional pathway 

of exposure to wildlife and humans. Air quality problems may arise from wind-driven salt particles 

containing selenium. Hence, given the scale of the project, there is a need to understand the wind 

patterns of the valley and the composition and physical properties of exposed salt or other solid waste 

products 

If 100,000 acres of land is retired under the Groundwater Quality alternative, then 13,406 lbs 

selenium/year in bio-waste needs disposal at the end of the waste-stream. At the end of a 50-year span 

of the project, 670,300 lbs selenium would need disposal to landfill. This amount would be available 

each 50 years into perpetuity. This magnitude of storage on land surface has long-term implications for 

the future of the western San Joaquin Valley as land-use changes take place. 

Calculation of the useful life of treatment facilities also would be a necessary to complete the 

depiction of overall treatment impacts to the landscape. Closure plans for evaporation ponds built for 

disposal of agricultural drainage in the Tulare and Kern subareas of the western San Joaquin Valley 

have been implemented in the past. However, the scale of decommissioning of proposed treatment and 

disposal areas would be of a much greater magnitude. 

27
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

Concluding Perspective 

The success of SLDFRE EIS alternatives and recently proposed drainage management plans 

relies heavily on above ground storage of salt and selenium and the development of successful 

technologies for selenium treatment and evaporation of water to concentrate salt. A scenario that 

successfully scales-up drainage water reuse, selenium bio-treatment, and evaporation of water to 

concentrate salt to magnitudes effective in treating planned volumes of drainflow may create new 

selenium exposure pathways that pose potential risks at levels that are currently undefined. However, 

selenium risk may be greatest at reuse areas. A 4,000-acre pilot project reuse area has consistently had 

significantly elevated selenium in bird eggs for the last five years. 

If selenium treatment is not ultimately successful the recent plan appears to rely upon increasing 

the amount of land retired. Land retirement, however, may be passive, may resolve only on-site 

drainage issues, and may not maximize the sustainability of agriculture, unless land is specifically 

retired to address a certain need and actively managed for a specific purpose (e.g., creation of habitat). 

The lack of a successful treatment technology for drainage also may ultimately mean an expansion of 

bare-soil evaporation within the valley. In contrast, a hydrogeologic approach with a regional 

groundwater management strategy has the potential to extend the viability of agriculture and minimize 

ecological risks of surface treatment and disposal. Further understanding of how ground-water flow is 

linked to selenium and salt transport would be necessary to quantify potential degradation of aquifer 

resources that might accompany such a regional program. 

Optimizing various drainage management paths to meet agricultural, environmental, and wateruse needs in the future may be better addressed by a more formal decision-making process. An 

approach such as Decision Analysis (refer to appendix B for a description of the components of 

Decision Analysis) could explicitly derive a mix of strategies with associated benchmarks, performance 

guidelines (e.g., triggers) and contingency options that would be needed to achieve a certain quantitative 

outcome. In essence, this type of approach would link models of such drainage reduction activities as 

conservation and reuse of agricultural water; land retirement; and groundwater extraction on a regional 

scale. A second tier of modeling would address selenium exposure (i.e., ecosystem scale models of how 

selenium is processed through valley food webs to vulnerable species of concern) to establish a firstorder understanding of relevant conditions, biological responses, and ecological risk should this revised 

proposal be implemented. Additional tiers of modeling would address other societal issues or issues of 

concern. Such balancing and selection of the mix of strategies of drainage reduction would support and 

document decision-making under the conditions of uncertainty and risk inherent in the proposed project. 

Specific drainage management pathways and associated goals for the proposed drainage 

management plan are: 

1. Measure acre-feet per acre to work towards achieving a specified drainage production rate (e.g., 

0.25 to 0.16 AF/acre/year). 

2. Track selenium and salt through implemented drainage reduction options (improved irrigation 

efficiency; shallow groundwater management; regional recycling; seepage reduction; and 

regional groundwater pumping) on a mass balance basis (i.e., measure volume or flow, 

concentration, and load) to work towards achieving load targets (lbs selenium or tons salt/acre or 

AF/year) based on AF/acre/year performance from above. 

28
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

3. Develop a land retirement selection plan with incentives to work towards achieving maximum 

containment of selenium in the aquifer by intentionally retiring large areas of land underlain by a 

shallow groundwater containing selenium concentration of > 50 μg/L. 

4. Decrease the attractiveness (e.g., netting of drainage ditches, hazing of birds) of reuse area as 

habitat for birds and wildlife to work towards achieving minimum selenium exposure in the 

environment. 

5. Develop bird and wildlife use models and monitor nesting to work towards achieving provision 

of mitigation habitat at a ratio appropriate in size to expected use. 

6. Develop contingency plans for accidental and natural flood events for each component of 

drainage reduction and disposal to work towards achieving protection against acute toxic 

episodes of selenium exposure. 

7. Track the composition (e.g., selenium and total dissolved solids) of waste-streams and quantify 

volumes, concentrations, and loads for disposal to work towards achieving optimal effectiveness 

and sufficient capacity of treatment technologies to meet drainage disposal requirements of 

volume, concentration, and load from above. 

8. Track acreage of solar evaporators, amounts of land-surface storage, and the hazardousness of 

solid material to work towards planning and achieving any additional societal land-use requests 

or requirements in the future. 

29
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

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Belitz, K., and Phillips, S. P., 1995, Alternative to Agricultural Drains in California's San Joaquin 

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Investigations Report, 88-4186, 129 p. 

HT Harvey and Associates, September 2004, San Joaquin River Water Quality Improvement Project, 

Phase I, Wildlife Monitoring Report 2003. Prepared by HT Harvey and Associates, Fresno, CA for 

Panoche Drainage District, Firebaugh, CA, 42 pp. 

HT Harvey and Associates, May 2005, San Joaquin River Water Quality Improvement Project, Phase I, 

Wildlife Monitoring Report 2004. Prepared by HT Harvey and Associates, Fresno, CA for Panoche 

Drainage District, Firebaugh, CA, 37 pp. 

HT Harvey and Associates. June 2006. San Joaquin River Water Quality Improvement Project, Phase I, 

Wildlife Monitoring Report 2005. Prepared by HT Harvey and Associates, Fresno, CA for Panoche 

Drainage District, Firebaugh, CA, 47 pp and attachment 

HT Harvey and Associates. November 2007. San Joaquin River Water Quality Improvement Project, 

Phase I, Wildlife Monitoring Report 2006. Prepared by HT Harvey and Associates, Fresno, CA for 

Panoche Drainage District, Firebaugh, CA, 60 pp. 

Presser, T.S., and Ohlendorf, H.M., 1987, Biogeochemical cycling of selenium in the San Joaquin 

Valley, California, USA: Environmental Management, v. 11, p. 805-821. 

Presser, T.S., 1994, The Kesterson effect: Environmental Management, v. 18, p. 437-454. 

30
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

Presser, T.S., and Piper, D.Z., 1998, Mass balance approach to selenium cycling through the San 

Joaquin Valley, sources to river to bay, in Frankenberger, W.T., Jr., and Engberg, R.A., 

eds., Environmental Chemistry of Selenium: New York, New York, Marcel Dekker Inc., p. 153-182. 

Presser, T.S. and Luoma, S.N. 2006, Forecasting selenium discharges to the San Francisco 

Bay-Delta Estuary: ecological effects of a proposed San Luis Drain extension, U.S. Geological Survey 

Open-File Report 00-416, 196 p. 

Purkey, D.R., and Wallender, W.W., 2001, Drainage reduction under land retirement over a shallow 

water table: Journal of Irrigation and Drainage Engineering, volume 127, no.1, pp.1-7. 

San Joaquin Valley Drainage Program, 1990a, A management plan for agricultural subsurface drainage 

and related problems on the westside San Joaquin Valley: San Joaquin Valley Drainage Program, 

Sacramento, California, 183 p. 

San Joaquin Valley Drainage Program, 1990b, Fish and wildlife resources and agricultural drainage in 

the San Joaquin Valley, California, volumes I and II: San Joaquin Valley Drainage Program, 

Sacramento, California, 878 p. and 2 appendices. 

 San Joaquin Valley Drainage Program, 1990c, Agricultural drainage treatment technology review: 

Memorandum Report, San Joaquin Valley Drainage Program, Sacramento, California, 183 p. 

San Joaquin Valley Drainage Implementation Program, 1998, Drainage management in the San Joaquin 

Valley - A status report: San Joaquin Valley Drainage Implementation Program, California, 

Department of Water Resources, Sacramento, California, 65 p. 

San Joaquin Valley Drainage Implementation Program, 1999, Land retirement technical committee final 

report: The San Joaquin Valley Drainage Implementation Program and the University of California 

Salinity/Drainage Program, 120 p. 

Schoups, G., Hopmans, J.W., Young, C.A., Vrugt, J.A., Wallender, W. W., Tanji, K.K., Panday, S., 

2005, Sustainability of irrigated agriculture in the San Joaquin Valley, California: Proceedings of the 

National Academy of Sciences. Volume 102. No. 43, p. 15352-15356. 

Skorupa, J.P., 1998, Selenium poisoning of fish and wildlife in nature: lessons from twelve real-world 

examples, in Frankenberger, W.T., Jr., and Engberg, R.A., eds., Environmental Chemistry of 

Selenium: New York, New York, Marcel Dekker Inc., p. 315-354. 

U.S. Bureau of Reclamation, 2001, Preliminary alternatives report, San Luis Unit Drainage feature reevaluation: U.S. Bureau of Reclamation Mid-Pacific Region, Sacramento, California, 132 p. 

U.S. Bureau of Reclamation, 2002, Plan formulation report, San Luis Unit drainage feature reevaluation: U.S. Bureau of Reclamation Mid-Pacific Region, Sacramento, California, 160 p. 

U.S. Bureau of Reclamation, 2004, Plan formulation report addendum, San Luis Unit drainage feature 

re-evaluation: U.S. Bureau of Reclamation Mid-Pacific Region, Sacramento, California, 6 chapter and 

appendices. 

U.S. Bureau of Reclamation, 2005, Draft Environmental impact statement on the San Luis drainage 

feature re-evaluation: U.S. Bureau of Reclamation, Mid- Pacific Region, Sacramento, California, 

1,591 p. 

U.S. Bureau of Reclamation, 2006, Final Environmental impact statement on the San Luis drainage 

feature re-evaluation: U.S. Bureau of Reclamation, Mid- Pacific Region, Sacramento, California, 

2785 p. 

U.S. Bureau of Reclamation, 2007, Record of Decision for the Final Environmental impact statement on 

the San Luis drainage feature re-evaluation: U.S. Bureau of Reclamation, Mid- Pacific Region, 

Sacramento, California, 37 p. 

U.S. Bureau of Reclamation, 2008, San Luis Drainage Implementation Plan (Handout #4) dated 

3/12/08. 

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Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

32

U.S. Department of the Interior, 1998, Constituents of concern: selenium, in Guidelines for 

interpretation of the biological effects of selected constituents in biota, water, and sediment, National 

Irrigation Water Quality Program Information Report No. 3: National Irrigation Water Quality 

Program, U.S. Department of the Interior, Washington, DC, p. 139-184. 

U.S. Fish and Wildlife Service Conceptual Monitoring, Compliance, and Adaptive Management Plan 

for the San Luis Unit Drainage Management Plan, December, 2007 draft; and February, 2008 draft: 

U.S. Fish and Wildlife Service, Sacramento, California, 75 pages and appendices
Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

Appendix A: Description of Drainage Management Alternatives and Plans 

 Land retirement alternatives have been refined throughout the development of SLDFRE 

EIS to accommodate requests for additional detailed alternatives that build on previous analyses of 

strategies. The definition of land retirement for some lands retired under different settlement 

agreements may include continuing the production of these lands through use of groundwater and water 

from sources other than from the Central Valley Project for irrigation. Land retirement alternatives 

analyzed and illustrated from the SLDFRE EIS (Section 2) are: 

In-valley (initial generalized alternative): Minimum land retirement assumption is 44,106 acres 

for the Westland Area for all action alternatives (common element) compared to existing conditions and 

No Action. Retired lands are assumed to be managed as dryland farming, grazed, or fallowed. Existing 

conditions in 2002 showed 20,518 acres subject to land retirement. The No-Action Alternative showed 

109,106 acres out-of-production. These acres include 65,000 acres as part of the WWD settlement; 

34,100 acres as part of the Sumner Peck Ranch et al settlement; 3,000 acres as part of the Britz 

Settlement; and 7,000 acres as part of the Reclamation CVPIA Land Retirement Program. 

Groundwater Quality Land Retirement Alternative:...“consists of retiring all the lands in 

Westlands with Se concentration greater than 50 ppb in the shallow groundwater and lands acquired by 

Westlands (that could be brought into production with drainage service, Table 2.3-1). It would also 

retire 10,000 acres in Broadview Water District in the Northerly Area. Total land retirement is about 

92,600 acres (44,106 plus additional 48,486 acres). This alternative includes irrigation system 

improvements to reduce deep percolation to shallow groundwater.” 

Water Needs Land Retirement Alternative:...“would retire lands such that the water needs of 

the lands remaining in production could be met by the Unit’s foreseeable water supply from its CVP 

contracts and groundwater resources. This results in an estimated 194,000 acres retired (44,106 plus 

149,850 additional acres). This estimate of land retirement is a planning level approximation and should 

not be viewed as a firm prediction of future water supply or water needs. For purposes of SLDFR 

analyses for plan formulation and this EIS, the Unit’s available water supply is based on the five 

districts receiving an average of 70 percent of their existing CVP contract amounts totaling 1,399,100 

AF/yr (or about 979,400 AF/yr) plus local groundwater supplies (about 185,000 AF/yr) for a total 

available water supply of 1,164,400 AF/yr. This acreage value would include lands with Se 

concentrations greater than 20 ppb in Westlands, lands acquired by Westlands (that could be brought 

into production with drainage service, Table 2.3-1) and 10,000 acres in Broadview Water District. The 

alternative would include irrigation system improvements to reduce deep percolation to shallow 

groundwater. The irrigation system improvement program would be similar to that described in Section 

2.4 for the In-Valley Disposal Alternative. 

 

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Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

Drainage-Impaired Area Land Retirement Alternative:...“would retire 308,000 acres (44,106 

plus 263,894 acres), including all of the drainage-impaired lands in Westlands –approximately 298,000 

acres. The Northerly Area (non-Westlands) is excluded from land retirement except for 10,000 acres in 

Broadview Water District. Drainage collection, treatment, and disposal facilities would not be needed in 

the Westlands drainage-impaired areas. The alternative would include irrigation system improvements 

to reduce deep percolation to shallow groundwater. The irrigation system improvement program would 

be similar to that described in Section 2.4 for the In-Valley Disposal Alternative, but would occur only 

in the Northerly Area. Lands remaining in production within the Northerly drainage-impaired area 

would be eligible for drainage service as under the previous alternative. The collection, treatment, and 

disposal of drainwater collected from drained lands would be only those needed to serve the Northerly 

Area 

SLU Plan proposed in USFWS Conceptual Monitoring, Compliance, and Adaptive Management 

Plan: 2/28/08 draft 

Table 1.Discrepancies between SLDFR in-valley alternatives and Westlands Drainage Plan. 

Plan Features SLDFR FEIS In-Valley/ 

Groundwater Quality 

Alternative 

SLDFR FEIS In-Valley/ 

Water Needs Alternative 

WWD 

Drainage Plan 

Acres with Tile Drains Installed 

(Northerly Area and WWD) 

187,116 122,833 122,8331

Acres of Land Retirement 92,592 (in WWD) 193,956 (in WWD and 

Broadview WD) 

100,0001

Drainage Volume before reduction 

(AF/Year) 

85,000 63,000 63,0002

# Of Reuse Areas (WWD) 14 13 151, 122

Acres of Reuse Areas (Northerly Area and 

WWD) 

16,700 12,500 12,5002

Drainage Inflow to Reverse Osmosis 

Treatment (Northerly Area and WWD) 

18,458 AFY 13,730 AFY 13,730 AFY1

Flowrate to Biotreatment (WWD) 5,179 AFY 2,815 AFY 2,815 AFY1,2

Drainage Inflow to Disposal Facilities 

(WWD) 

5,179 AFY3 2,815 AFY3 5,500 

AFY2

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Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

SLU Plan proposed in USBR Handout #4, San Luis Unit Drainage Implementation Plan, dated 

2/12/08. 

Table I-1 below identifies the proposed system drainwater reduction and treatment capability consistent with projected future 

on-farm operations at full capacity 

Table I-1 

Component Characteristic Value 

Drainage Area Acres w/ tile drains 122,833 

On-Farm Drainwater Reduction Volume reduced per year (AF) 2,970 

Regional Drainwater Reduction Volume reduced per year (AF) 4,200 

Other Drainwater Reduction Volume reduced per year (AF) 10,350 

Drainage Rate After above Reductions Drainage Volume per year (AF) 45,287 

Drainage Reuse 

Vol. reduction Westlands per yr (AF) 12,827 

Drainage Rate After Reuse Volume in AF/yr (average) 13,730 

Flow rate in cfs (average) 19.0 

Drainage Treatment 

(Current Est.) 

Initial average Se concentration of reused 

drainwater (μg/L) 

120 

Final average Se concentration of reused 

drainwater (μg/L) 

270 

Volume to RO treatment per year (AF) 13,730 

Volume to Se biological treatment per year (AF) 6,865 

Average Se concentration in influent to solar evap 

units (μg/L) 

10 

Initial average TDS concentration at point of 

discharge (mg/L) 

13,700 

Final average TDS concentration at point of 

discharge (mg/L) 

27,600 

Land Conveyance Miles of pipe <71 

Miles of canal 0 

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Technical Analysis of In-Valley Drainage Management Strategies for the Western San Joaquin Valley—May 16, 2008 

Appendix B: Decision Analysis Modeling 

As an Adaptive Management tool Decision Analysis would: 

• formalize data-gathering, planning, and implementation decisions and analyze their 

consequences on appropriate scales (i.e., local, regional, and state); 

• organize individuals and their expertise into a working group whose members are encouraged to 

investigate the relationships between their disciplinary boundaries in a way that makes the 

overall model and solution pathways more relevant and durable. 

Thus, Decision Analysis would involve all agencies and stakeholders in a quantitative and an 

analytically-focused overarching vision of the challenges and risks at hand. In turn, an integrative 

scientific basis of understanding is built to enable consensus-building and inform cooperative 

monitoring and compliance activities. 

Decision Analysis is tailored to the specific decision being addressed, but it generally follows 

five steps: 

 Frame the Problem. Identify the decision context, the decision-makers(s), and stakeholders. 

The purpose of this step is to develop a clear statement of the decisions being addressed, and to identify 

the roles, goals, and interests of the decision-makers and stakeholders in the overall process. 

 Identify Objectives, Alternatives, and Uncertainties. A fundamental feature of the Decision 

Analysis approach is the decomposition of any decision problem into three basic components: what the 

decision maker wants (his or her objectives), what they can do (the decision alternatives), and other 

factors that the decision-maker does not control but that can affect the outcome of a decision 

(uncertainties). Developing a clear identification and statement of each of these components is critical 

to being able to conduct a useful analysis. Depending on the decision context, this step may include 

active participation of multiple stakeholders; stakeholders have an important role in identifying 

objectives, they may have a role in identifying alternatives, and they may also bring technical 

knowledge that is useful in identifying and quantifying uncertainties. 

 Build a Decision Model. Decision Analysis modeling is a process of quantifying the 

relationships between the decision alternatives and the ability for each alternative to meet the decisionmakers and/or stakeholders objectives. Only very rarely is there an unambiguous relationship between 

an alternative and the outcome of choosing that alterative – typically there are a variety of uncertainties

that intervene, where the outcome of a particular alternative depends on things not fully understood at 

the time the decision must be made. Depending on the decision context, relevant uncertainties may 

include scientific uncertainties about the state of the physical and biological processes involved, “state 

of the world” uncertainties about, for example, future weather patterns or climate, policy-related 

uncertainties about, for example the future regulatory environment, and so forth. Building a decision 

model first requires specifying the relationships between the decision alternatives, uncertainties, and 

objectives, and then quantifying those relationships and the uncertainties. Quantification in a Decision 

Analysis model means both estimating the likelihood of various outcomes for a given uncertainty, and 

quantifying how well each alternative will perform against the specified objectives under each potential 

outcome of the uncertain factors. Decision Analysis includes a wide array of tools and processes to 

facilitate the model-building process. 

 

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37

 Conduct Analyses and Sensitivity Analyses. Once a model is built, there are many types of 

analyses that can be conducted to inform the decision-makers and stakeholders. The most appropriate 

and useful analyses depend on the decision context. For most real-world decision contexts there are 

multiple parties involved, multiple objectives are relevant, and there may be varying degrees of 

confidence in the quantification of the uncertain factors. In those cases, more sophisticated analyses and 

sensitivity analyses are necessary to fully elucidate the problem. Some examples of sensitivity analyses 

include: 

9 Full quantification of the probability and net benefits of each alternative (in addition to 

calculation of the expected value): This is helpful in identifying situations where, perhaps, one 

alternative has a higher expected value, but with the potential for very good or very bad 

outcomes (a high variance alternative), and another alternative with a lower expected value has 

much less uncertainty about the outcome (a low variance alternative). 

9 “Importance analyses” identifying the input uncertainties that have the most impact on the 

uncertainty in the outcomes: These analyses may point to areas of further research that would 

reduce the uncertainty about the outcome of a particular decision. 

9 Decision policy uncertainty analyses, which are similar to importance analyses but focus on 

identifying which uncertainties are “decision relevant”: Decision-relevant uncertainties are 

those where the optimal decision is different depending on the outcome of that uncertainty. 

 Decide and Execute. Ultimately, of course, the goal of Decision Analysis modeling is to 

support a decision or the selection of a preferred alternative. Like all models, however, Decision 

Analysis models are simply tools to be used by the decision-maker(s). No tool can “make a decision,” 

but a high-quality Decision Analysis model can be used by the decision-makers to explore the 

implication of various choices in terms on the impact on objectives that they themselves specify based 

on their understanding of the science and what the future state of the world looks like.