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Marine sedimentary rocks of the Coast Ranges contribute selenium
to soil, surface water, and ground water in the western San Joaquin
Valley, California. Irrigation funnels selenium into a network of subsur-
face drains and canals. Proposals to build a master drain (i.e., San Luis
Drain) to discharge into the San Francisco Bay-Delta Estuary remain as
controversial today as they were in the 1950s, when drainage outside
the San Joaquin Valley was first considered. An existing 85-mile portion
of the San Luis Drain was closed in 1986 after fish mortality and deformi-
ties in ducks, grebes and coots were discovered at Kesterson National
Wildlife Refuge, the temporary terminus of the drain. A 28-mile portion
of the drain now conveys drainage from 100,000 acres into the San
Joaquin River and eventually into the Bay-Delta. If the San Luis Drain
is extended directly to the Bay-Delta, as is now being proposed as an
alternative to sustain agriculture, it could receive drainage from an esti-
mated one-million acres of farmland affected by rising water tables and
increasing salinity. In addition to agricultural sources, oil refineries also
discharge selenium to the Bay-Delta, although those discharges have
declined in recent years. To understand the effects of changing selenium
inputs, scientists have developed the Bay-Delta Selenium Model.
U.S. Department of the Interior
U.S. Geological Survey
Fact Sheet 2004-3091
August 2004
Linking Selenium Sources to Ecosystems:
San Francisco Bay-Delta Model
The Bay-Delta Selenium Model is a systematic linked approach for
conducting forecasts of selenium (Se)
effects on aquatic food webs including
higher trophic level animals such as birds
and fish (Luoma and Presser, 2000). The
methodology is presented as a new tool
to predict ecological effects based on the
major processes leading from loading
through consumer organisms to preda-
tors. The approach is illustrated here and
can be used with any set of explicitly
stated conditions. Forecasts obtained
from the Bay-Delta Selenium Model con-
sider (1) loads, (2) water column concen-
trations, (3) speciation, (4) transforma-
tion to particulate forms, (5) particulate
concentrations, (6) bioaccumulation, and
(7) trophic transfer to predators, in addi-
tion to traditional considerations of water
supply and drainage demand.
Major inputs used to determine a
composite input load are (1) agricul-
tural drainage via direct discharge to the
Bay-Delta; (2) effluents from the North
Bay oil refineries; (3) San Joaquin River
inflows which include agricultural drain-
age; and (4) Sacramento River inflows.
Historical analyses of drainage needs
were used to identify the most likely Se
loads that would be carried outside the
San Joaquin Valley via a conveyance
discharging a constant load and convey-
ance via the San Joaquin River. Selenium
concentrations and forms in the Bay-
Delta are forecast, then those concentra-
tions are used to model bioaccumulation
in invertebrates, like clams. Transfer
from clams to predators is estimated from
field data, and Se effects on predators are
then forecast from data in the existing
literature. Data gathered during the years
prior to refinery cleanup helped check the
model and provide a baseline for deter-
mining site-specific effects.
The Se load delivered to the Bay also
depends on the amount of flow from the
San Joaquin River that passes through
the Delta and the amount recycled south
through the Delta and Tracy pumping
stations. The protocol for linking Se load
and Se concentration under assigned
hydraulic conditions and time duration is:
composite freshwater endmember concentration
= composite input load/composite input volume
The projections or outputs of the
model are presented by season, where a
season is defined as six months of pre-
dominantly high river inflows (December
through May) or six months of predomi-
nantly low river inflows (June through
November). Riverine influences also
depend upon water year type. In combi-
nation with flow seasons, forecasts are
made for critically dry years or for wet
years. A wide range of agricultural Se
input loads is possible, depending upon
which management strategies are chosen.
Potential ranges of annual input loads
were derived assuming Se discharge was
continuous and are presented here as
discharged load per six months (i.e. one-
half the annual load under a constant rate
of loading).
The model allows consideration of
many different drainage options (Luoma
and Presser, 2000). In general, most
options that meet existing demand for
drainage appear to pose strong risks to
the reproduction and survival of sensitive
birds and fish. Threats to reproduction and
survival of birds and fish are particularly
severe during periods of low river flow.
Vulnerable species include diving ducks,
white sturgeon and Sacramento splittail.
Example Selenium Forecast for the
San Francisco Bay-Delta
An example forecast is shown (oppo-
site page) for a dry year during the low
flow season and with conveyance through
a San Luis Drain extension directly to the
Bay-Delta. The dry years and low flow
seasons will be the ecological bottle-
neck (the times that will drive impacts)
with regard to Se. Surf scoter, greater
and lesser scaup, and white sturgeon are
present in the estuary during the low flow
season and leave before high flows sub-
side. Animals preparing for reproduction,
or for which early life stages develop
in September through March, will be
vulnerable.
The example forecast shows Se
concentrations for each media forecast
(water, particulate, invertebrate, preda-
tor), along with guidelines or concentra-
tions where biotic effects are expected
(Luoma and Presser, 2000). The fore-
casts show conditions at the head of
the estuary for a range of inputs (6,800;
18,700; or 44,880 pounds Se released
per six months) from the San Luis Drain
and for a small amount of San Joaquin
River inflow to the Bay. The input from
oil refineries is assumed constant at 680
pounds Se per six months. We assume a
partitioning coefficient (Kd) of 3 x 103
typical of Bay-Delta shallow sediment
conditions and a generic bivalve assimi-
lation efficiency (AE) of 0.55 to reflect
particulate transformation and bioaccu-
mulation potential from a sediment with a
mixture of forms.
In general, the lowest guideline values
for waterborne, particulate, dietary, and
predator tissue Se are exceeded in every
forecast considered in the figure where
the input is from a proposed San Luis
Drain extension. The highest guide-
lines from the literature are exceeded in
all forecasts except that for the lowest
load considered (6,800 pounds per six
months) where exceedance does occur for
particulates, white sturgeon, and greater
and lesser scaup liver. If a San Luis Drain
extension is constructed and if it dis-
charges the quantities of Se predicted in
our simulation scenarios, during low flow
seasons, a high hazard seems likely, with
threats to fish and bird species under the
load scenarios tested here.
Forecast simulations also were con-
ducted for loading via the San Joaquin
River (Luoma and Presser, 2000). If
careful management of an out-of-valley
resolution to the drainage problem results
in discharges of Se via the San Joaquin
River to the Bay-Delta (for example at
3,500 pounds per six months), the risks
are less than those forecast for a San Luis
Drain extension. Under the low flow
season of a dry year scenario, the Se con-
centrations forecast in prey and predators
are similar to Se concentrations observed
during conditions in the Bay-Delta prior
to refinery cleanup. Selenium contami-
nation documented from 1986 to 1996
was sufficient to threaten reproduction in
key species within the Bay-Delta estuary
ecosystems and resulted in human health
advisories being posted for consumption
of those species.
The San Luis Drain transports selenium-laden agricltural drainage from the western San Joaquin
Valley. Agricultural drainage waterways are posted with a state fish and waterfowl consumption
advisory because of selenium.
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The Bay-Delta is probably best
suited for site-specific Se guidelines and
the Bay-Delta Selenium Model could
provide a framework for developing
new protective criteria. If water quality
criteria are to be employed in managing
Se inputs, then consideration should be
given to the elevated Se concentrations
currently occurring in clams and fish of
the Bay-Delta, even though waterborne
Se concentrations in the Bay-Delta are
less than recommended criteria (Luoma
and Presser, 2000).
Monitoring Recommendations
A long-term monitoring program is
crucial to understanding the fate and
impact of management changes for
protection of ecosystems receiving Se
discharges. Monitoring, as conceptu-
alized below, would sample critical
environmental components at a frequency
relevant to each process to determine
trends in Se contamination or changes in
processes that determine fate and effects
of Se (Luoma and Presser, 2000).
A linked or combined approach
would include all considerations that
cause systems to respond differently to Se
contamination.
• In any site-specific analysis of Se
impacts, it is important that “site” be
defined by all hydrologically relevant
components. Hydrologic models would
serve as a basis for developing this
infrastructure. Specifically, the Bay-Delta
ecosystem is connected to the San Joa-
quin River ecosystem. The Delta is the
transition zone between the Bay and the
largest potential source of Se (i.e., agri-
cultural drainage from the San Joaquin
Valley via either a dedicated drain or the
San Joaquin River).
• The vulnerability of downstream
water bodies should be considered when
evaluating upstream source waters. Tox-
icity problems may not appear equally
in all “site” components because some
components may be more sensitive than
others. For example, the San Joaquin
River, as a flowing water system may be
less sensitive to Se effects (especially if
selenate dominates inputs) than adjacent
wetlands, the Delta or the Bay, where resi-
dence times and biogeochemical transfor-
mations of selenate are more likely.
• Any analysis of Se effects must
take into account the influences of vari-
able river inflows. Selenium impacts in
the Bay-Delta could increase if water
diversions increase or if San Joaquin
River inflows increase with concomi-
tant increases in Se loading (i.e. the Se
issue and the water management issues
are tightly linked). The most significant
impacts of irrigation drainage disposal
into the Bay-Delta will occur during low
flow seasons and especially during low-
river flow conditions in dry or critically
dry years. Dry or critically dry years
have occurred in 31 of the past 92 years,
with critically dry years comprising 15 of
those years.
• Establishing a mass balance or
budget of Se through the estuary is
crucial because internal (oil refinery) and
external (agricultural drainage) sources
of Se are changing as a result of manage-
ment. At a minimum, a mechanism for
tracking Se loading via oil refineries and
the San Joaquin River is needed based on
San Joaquin River, Sacramento River, and
Bay-Delta hydrodynamics. Monitoring
programs need to measure the on-going
status of the system in terms of inputs,
storage in sediment, through-put south via
the Delta-Mendota Canal and California
Aqueduct, and through-put north to the
Bay.
• Storms and high-flow years will be
times of increased regional discharge of
San Joaquin Valley drainage containing
high concentrations and loads of Se. Simu-
lations predict if the precipitation-depen-
dence of agricultural Se inflows is not
recognized, violations of upstream water
quality criteria and load targets could
result on a recurring basis. The long-term
effects of such occurrences on wetlands,
wetland channels, the Delta and the Bay
need to be better understood. The pos-
sibilities of long-term storage after such
conditions and the efficiency of bioac-
cumulation during varying conditions of
flow should be studied.
• Multiple-media guidelines, in combi-
nation, provide a feasible reference point
for monitoring. The critical media defined
here are water, particulate material, and
prey and predator tissue. Monitoring plan
components necessary for a mass balance
approach include source loads; concen-
trations of dissolved Se and suspended
Se; Se speciation in water and sediment;
assimilation capacities of indicator food
chain organisms; and Se concentrations
in tissues of prey and predator species.
• Determination of transformation
efficiency and processes that determine
Kds (distribution or partitioning coef-
ficients) of Se in the Bay-Delta and San
Joaquin River are crucial to relate loads
to bioaccumulation, rates of transfer, and
effects. Trace elements sequestered in
bed sediments and in algal mats would
be a part of recommended mass balance
considerations.
• Invertebrates may be the optimal
indicator to use in monitoring Se because
they are practical to sample and are
most closely linked to predator expo-
sure. Knowledge of optimal indicators
in the Bay-Delta and San Joaquin River
are necessary to fully explore feeding
relations. Resultant correlations with Se
bioaccumulation in food webs are a part
of this process.
• Determination of food web inter-
relations would help identify the most
vulnerable species. Specific protocols
that include life cycles of vulnerable
predators including migratory and mobile
species would then document Se effects
for the species most threatened.
• If management and regulatory
measures to restore the San Joaquin River
ecological resources to their former level
of abundance are to be effective, then
the biogeochemistry of Se, ecological
processes, and hydrodynamics in this
system must be further investigated and
understood. Adaptive management and
monitoring for the San Joaquin River
should be based on the biotransfer of Se
and consideration of the environmental
stresses imposed by present degraded
conditions. Current discharge of agricul-
tural drainage to the San Joaquin River
via a 28-mile section of the San Luis
Drain is under monthly and yearly load
limitations. To determine whether load
manipulation actually protects vulnerable
predators, the following monitoring plan
components are needed:
1. Identification of vulnerable food
webs
2. Identification of sites most at risk
from impacts of agricultural drainage
3. Analysis of effects on predators that
includes food web components
4. Identification of elevated risk peri-
ods for effects based on hydrodynam-
ics
5. Calculation of protective loads/con-
centrations based on bioaccumulation
in prey
• In view of the analysis of the existing
Se reservoir in the San Joaquin Valley, con-
sideration of the degradation of ground-
water aquifers needs to be a factor in
management scenarios. Short-term man-
agement that results in more storage than
leaching will result in more degradation
of aquifers. Mass balance considerations
should include a “storage” term, not only
input and output terms. Monitoring and
assessment of storage may help determine
if treating discharge on an annual basis
will suffice to manage the current regional
imbalance of water, salt, and Se.
• Treatment may also be important in
determining source load impacts. Treat-
ment technologies applied to source waters
may affect both the concentration and
speciation of the effluent. For example, a
treatment process could decrease the con-
centration of Se in the influent, but result
in enhanced Se food chain concentrations
if speciation in the effluent changes to
increase the efficiency of uptake.
Theresa S. Presser and Samuel N. Luoma
National Research Program
Water Resources Division
Menlo Park, CA 94025
Summary of Selenium Issues in California
• Accurate forecasting of the environmental fate of selenium (Se) in the San
Francisco Bay-Delta Estuary is crucial because of the element’s effect on
reproduction in aquatic birds and fish.
• Internal and external sources of Se to the estuary are changing due to
water management changes related to the restoration of the San Joaquin
River and Bay-Delta.
• Current projects allow discharge to the estuary of saline subsurface
waters from the western San Joaquin Valley via the San Joaquin River.
Direct conveyance of agricultural drainage to the estuary could occur if an
extension of the San Luis Drain is built and discharge permits approved.
• The U.S. Environmental Protection Agency is re-evaluating Se standards
for the protection of fish and wildlife. The U.S. Fish and Wildlife Service
and the National Marine Fisheries Service through the California Toxics
Rule are asking for more stringent Se criteria.
• Selenium concentrations were less than water quality guidelines in both
the Delta and the Bay in the latest surveys in 1996. Nevertheless, Se in the
food web was sufficient to be a threat to some species and a concern to
human health if those species were consumed.
Cooperators:
1. U.S. Environmental Protection Agency
(Region 9, Water Division)
2. Contra Costa County
3. Contra Costa Water District
Reference and for additional information:
Forecasting Selenium Discharges to the San Fran-
cisco Bay-Delta Estuary: Ecological Effects of A
Proposed San Luis Drain Extension, by Samuel
N. Luoma and Theresa S. Presser, U.S. Geological
Survey Open-File Report 00-416.
http://water.usgs.gov/pubs/ofr00-416/
or contact: tpresser@usgs.gov
snluoma@usgs.gov
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