Note: This project is being jointly carried out by USGS and UC Davis.
The Principal Investigator (P.I.) for USGS is Celia Zamora. The P.I. for UC Davis is
Dr. Randy Dahlgren.
This project addresses drinking water and aquatic habitat issues associated with nitrate and
organic carbon in the lower San Joaquin River (SJR). The primary drinking water issue with
nitrate in the lower SJR is the role of nitrate in stimulating algal growth which affects
the cost and effectiveness of water treatment downstream. Organic carbon is a drinking water
issue because of the potential for forming disinfection byproducts when the water is treated.
In addition to the drinking water issues, the nutrient inputs to the SJR and the resultant
algal growth contribute to low dissolved oxygen concentrations in the SJR near Stockton which
can be deleterious to Chinook salmon migration.
Based on previous work by the project team (Kratzer and others, 2004; Burow and others, 1998;
Kratzer and Shelton, 1998; Phillips and others, 1991), it appears that the long-term increase
(over 50 years) in nitrate concentrations in the SJR are currently mostly due to ground-water
sources. In fact, the range of 15N and 18O values of nitrate in river samples collected in
2000 and 2001 suggest that animal waste or sewage was the most significant source of nitrate in
the river at the time (Kratzer and others, 2004). There are several dairies close to the SJR on
the east side that could contribute to the nitrate in the river. The goal of this study is to
use three approaches to address the question of nitrate in ground-water accretions and the
source of that nitrate. The three approaches are necessary to capture the different scales of
spatial and temporal variability, as well as accurately quantify nitrate sources and loads. The
first approach involves doing a reconnaissance by boat to get a qualitative, semi-quantitative
sense of significant ground-water inflow areas to the river by continuously measuring the water
temperature, electrical conductivity (EC), and optical properties of water just above the
streambed. Areas with significant changes in any of these parameters will be further evaluated
and samples collected of the ground water inflow for stable isotopes of carbon, nitrogen, and
oxygen, as well as other chemical indicators diagnostic of source. The second approach is to
re-visit three sites in the SJR where nested monitoring wells were installed in the late-1980s
in the streambed and on both banks and to install three more sites in the river. The established
sites were modeled during an extended dry period. The six sites will give a better spatial
coverage of the study area and will allow a comparison of present conditions to the late-1980s.
The third approach is to extend a synoptic sampling method recently used on the lower Merced
River as part of the San Joaquin National Water-Quality Assessment (NAWQA) program to the SJR
study area. The approach will be to sample at about 30 sites between the 6 permanent sites in
the late summer in 2007 and in 2008. At each site, a manometer with a drive-point is used to
evaluate hydraulic gradients below the streambed. Also, temperature differences between the
river and below the streambed are evaluated and samples are collected from below the streambed
in gaining reaches to sample for nitrate and organic carbon concentrations.
Nitrate and organic carbon levels in the SJR are of concern to the Central Valley Regional Water
Quality Control Board (Regional Board) and to the CALFED Drinking Water Quality Program (DWQP)
because of their impacts on the cost and effectiveness of water treatment for drinking water and
on the dissolved oxygen levels in the Stockton Deep Water Ship Channel (DWSC). Nitrate and organic
carbon are pollutants of concern for the CALFED DWQP and this study addresses one of that
program’s top priorities: monitoring, assessment, and research projects that increase
our understanding of sources, transport, transformation, and fate of the CALFED drinking water
quality pollutants of concern. This study also addresses several of the Regional Board priority
projects including the development of a Total Maximum Daily Load (TMDL) for the low dissolved
oxygen in the Stockton DWSC. It appears that ground water could be a major source of nitrate to
the SJR, supporting algae growth that can eventually lead to water treatment concerns and to
oxygen depletion in the Stockton DWSC. This oxygen depletion in the Stockton area can be deleterious
to Chinook salmon migration. This study was designed primarily to address the issue of nitrate
sources to the SJR; organic carbon will be analyzed at the same time to further define its sources
to the SJR. The study area for this project is the SJR from just upstream of the confluence of
Salt Slough to the new California Department of Water Resources (DWR) water quality sampling site
near Vernalis, about 60 river miles.
The objective of this project is to quantify the amount of ground-water accretions to the lower
SJR and its nitrate and organic carbon concentration using multiple lines of evidence. In
addition, isotopic and optical characteristics of the ground water will be compared to various
end-members to identify the sources of nitrate in the ground-water accretions.
The study area for this proposal is the SJR from just upstream of the confluence of Salt Slough
to the new DWR water quality sampling site near Vernalis, about 60 river miles. A complete
description of the study area can be found in Gronberg and others (1998).
The idea of conducting a boat reconnaissance was originally presented to the Principal
Investigator by Dr. Vance Kennedy, a retired research hydrologist with the USGS in Menlo Park
and currently a farmer in the Modesto area. While at the USGS, Dr. Kennedy’s research
concentrated on the use of tracers to understand the movement of both solutes and solids in
the natural environment. Conducting boat reconnaissance trips adds spatial measurements of
ground-water sources throughout the entire study area. This task adds a more qualitative,
semi-quantitative measure of significant ground-water inputs between specific points measured
at the monitoring-well and synoptic sites. The desired outcome of this task is to be able to
use the boat measurements to extrapolate the results from the monitoring-well and synoptic sites
to the entire study area.
We will attempt to identify the locations of ground water “hot spots” using a
combination of in-situ water temperature, EC, and optical property measurements. Previous
studies have demonstrated that ground-water and dairy-runoff inputs may be identified in the
field using a combination of these measurements (Bergamaschi and others, 2005; Constantz and
Thomas, 1996; John Vaccaro, Hydrologist, USGS Tacoma, WA, pers. comm., 2005; Lee, 1985; Harvey
and others, 1997; USEPA, 2000). A boat specially fitted to make continuous measurements of
position, water temperature, EC, and optical parameters near the streambed will survey the SJR
by slowly traveling downstream, identifying the location of inputs in real time by the observed
changes in measured river water values. The boat reconnaissance trips will be coordinated with
the synoptic samplings at about 30 sites. This will occur during late summer in 2007 and in
2008, depending on flows and other factors.
The boat reconnaissance approach to identifying ground water “hot spots” has been
applied a few times in the past 20 years (USEPA, 2000). In a USEPA sponsored workshop on
ground water-surface water interactions in 1999, the approach was referred to as “sediment
probes” or “drag probes” in a scientific paper and in two summary sessions on
available methods (USEPA, 2000). John Vaccaro of the USGS Washington WSC has identified ground
water “hot spots” in the Yakima River Basin using a boat reconnaissance approach
with temperature and EC probes. John felt confident that we would be able to identify ground
water “hot spots” at times of year with relatively large differences between ground
water and surface water temperatures and(or) EC (John Vaccaro, Hydrologist, USGS Tacoma, WA,
pers. comm., 2005).
Once a ground-water input location is identified, a relatively pure ground water sample will
be pumped from below the streambed using a temporary drive-point with tubing attached. This
sample and the surface water at the site will be analyzed for a variety of chemical tracers
(15N,18O, and 17O of nitrate, 15N of DON, 13C of DIC and DOC, 18O and 2H of water, and
molecular composition)(Bergamaschi and others, 2000; Kendall, 1998). Each of these
tracers has proven useful in previous studies for discrimination between the biological and
geochemical signatures of the presumptive sources. Comparison of parameter values to
those of separately-collected source samples will allow us to relate the chemical signature
of sources to the chemical signature of localized input water samples. Although 17O of nitrate
will be analyzed for many surface water samples to see if atmospheric nitrate might be
important, only a few ground water samples will be analyzed for 17O of nitrate.
The use of nested monitoring wells in the river and on both banks was used by Phillips and
others (1991) in the late-1980s to model ground-water inputs to the SJR. This project will
further develop this research. The data collected at the six sites will allow for the
modeling of ground-water inputs and their associated water quality and comparison of results
to values from the late-1980s.
Three existing sites and three new sites are being monitored for the vertical hydraulic and
temperature gradients beneath the streambed, and being used for retrieving ground-water
samples. Ground-water quality data collected from these sites will be used to estimate
nitrate and organic carbon concentrations in ground water. Hydraulic gradient and temperature
data will be used to determine the rates of ground- water flow into the river. These flux rates
will be combined with the water-quality data to estimate the amount of nitrate and organic
carbon contributed to the river from ground water.
The existing monitoring wells (on the river banks) associated with the previously established
transects were rehabilitated and developed, and instrumented with continuous water level
sensors. These 14 bank wells were first sampled in September 2006. Paired monitoring wells were
installed at different depths below the streambed at all six sites in the SJR. These
streambed monitoring wells were instrumented with continuous temperature and water level
sensors. These 12 in-stream wells were first sampled in May 2007. The following monthly
measurements are being made at the 26 monitoring wells: field parameters; water levels; and
nutrients and organic carbon. Quarterly samples are being collected for analysis of major ions;
isotopes; trace elements; and nitrogen gas. All samples from the monitoring wells are being
collected by UC Davis. We will collect 20 months of measurements at the 26 monitoring wells,
from September 2006 through January 2009.
The rate of ground-water inflow to the river will be estimated using two numerical methods:
simulation of vertical flow and energy (heat) transport beneath the streambed at the six
stationary sites and simulation of two-dimensional ground-water flow along the three existing
transects. Flow and heat transport will be simulated in one dimension at each of the streambed
monitoring-well sites using available USGS code. This method provides a relatively inexpensive
means to estimate fluxes and to gain understanding of the complex interactions between streams
and the adjacent aquifer (Constantz and Thomas, 1996). Based on previous estimates of ground-water
flux into the SJR (Phillips and others, 1991), estimates of average inflow on the order of 10
cm/day/unit area are large enough to simulate advective-dominated heat transport using these
methods.
Two-dimensional steady-state flow along the three existing transects, and associated average
river-aquifer interaction during the study period, will be simulated using the models
developed by Phillips and others (1991). The transect models in the previous study represented,
and were calibrated for, drought conditions. Conditions during this study period follow
an extended period of more normal rainfall conditions. The hypothesis is that the previous models
are reasonable representations of the natural system and will simulate adequately the changes in
hydraulic conditions near the river with justifiable changes in boundary fluxes representing
recharge and ground-water pumpage. If such changes in flux do not result in a reasonable
representation of conditions during the study period, the models will be considered inadequate
for representing these conditions. If the models are not adequate, there will be greater
reliance on other methods presented herein; a full re-calibration of the transect models is beyond
the scope of the proposed work.
The idea of synoptic measurements came from the recent NAWQA work on the Merced River (Capel and others, 2008; Essaid and others, 2008; Puckett and others, 2008). This NAWQA work used synoptic measurements of hydraulic gradients, temperatures above and below the streambed, and nitrate and dissolved oxygen concentrations below the streambed to provide better spatial coverage around the permanent transects for a study of ground-water/surface-water interactions (Gronberg and others, 2004). In this study, these synoptic sites will provide valuable data on hydraulic gradients and ground-water quality between permanent sites. They will also hopefully correlate with the continuous boat reconnaissance data to allow an extrapolation. The desired outcome of this approach is to fill spatial gaps for water quality and hydrologic data and to allow extrapolation of results from the other two approaches.
Synoptic measurements are being taken at about 30 sites in the study area. These sites are spaced approximately every 2 river miles throughout the study area, except near points of interest where they are closer. The synoptic events are coordinated close in time to the boat reconnaissance trips. The sampling at each site includes measurements of hydraulic gradients, temperatures above and below the streambed, nitrate and organic carbon concentrations below the streambed, and isotopes. These samples are obtained by use of temporary drive-points with tubing attached as with the ground-water samples in the boat reconnaissance. These synoptics provide more quantitative water quality data on ground-water inputs than the boat reconnaissance and better spatial coverage than the six permanent monitoring-well sites. However, they do not provide the temporal coverage of the permanent sites.
Nutrient analyses and major ions and selected trace elements (especially selenium, boron, and molybdenum) are being done at a UC Davis laboratory under the guidance of Dr. Randy Dahlgren. Organic carbon analyses are being done at either the UC Davis laboratory or the California Water Science Center Laboratory (see Bird and others, 2003 for organic carbon method). Isotope analyses are being done at the Menlo Park Stable Isotope Laboratory. Field measurements (including EC, temperature, and ultraviolet absorbance) are made by continuous monitors and multi-parameter probes. The continuous monitors at the monitoring-well sites (temperature and pressure transducers) are maintained by USGS field staff in the same manner as was done for the NAWQA study on the Merced River. This continuous data is being stored in ADAPS in the same manner as was done for the NAWQA study.
All sites at which water-quality data are collected in this project have official USGS site identification numbers and the data are being entered into NWIS. This includes all boat reconnaissance sites where water-quality samples are collected by drive-point or from the adjacent surface water; all fixed sites as part of the monitoring-well approach; and synoptic sites with water-quality data collected by drive-point. Quality-control samples (blanks and replicates) are being collected on at least 15 percent of all water-quality samples, more frequently for isotope samples run at the Menlo Park Stable Isotope Laboratory. Continuous monitors (boat reconnaissance and monitoring wells) and multi-parameter probes (synoptics) are being calibrated according to guidelines established in Wagner and others (2000).
Streamflow data required for the project will be obtained from existing USGS and DWR gages on the SJR (listed here from upstream to downstream):
- SJR near Stevinson (DWR; 11260815)
- SJR at Fremont Ford Bridge (USGS; 11261500)
- SJR near Newman (USGS; 11274000)
- SJR near Crows Landing (USGS; 11274550)
- SJR near Patterson (DWR; 11274570)
- SJR at Maze Road Bridge (DWR; 11290500)
- SJR near Vernalis (USGS; 11303500)
The Principal Investigators for two related projects (Thomas Harter of UC Davis and Carol Kendall of USGS) dealing with agricultural land uses in the San Joaquin Valley and their impacts on water quality decided that a joint technical advisory committee (JTAC) made a lot of sense for disseminating information and getting feedback. JTAC membership will be solicited from the agricultural community (county farm bureaus, irrigation districts, county agricultural commissioners, UC cooperative extension, etc.), regulatory agencies (Regional Board, USEPA, etc.), resource agencies (DWR, USBR, etc.), and universities. A meeting of the JTAC is anticipated during the fall in 2008. In addition, study researchers will make periodic presentations to various stakeholder and professional groups. The desired outcome of these efforts is to keep the JTAC and other interested parties informed about the project and to receive valuable guidance and assistance. The desired result of these efforts is that the study will be accepted and used by both the agricultural community and regulatory agencies to implement measures to reduce nitrate inputs to the SJR.
The USGS Principal Investigator submits quarterly progress reports to UC Davis. A JTAC meeting and several presentations to various scientific and stakeholder groups are anticipated during the study. A draft USGS report (Scientific Investigations Report) summarizing all results from the project will be completed in 2009. This report will be a collaborative effort with UC Davis researchers. Depending on the findings, three journal articles may also be prepared in collaboration with UC Davis researchers – one on each approach used in the project (boat reconnaissance, monitoring wells, and synoptics).
The total budget for the study is $977,500. UC Davis signed an agreement with the SWRCB on 12/5/05 for this amount of funding. On 6/15/06 the USGS and UC Davis signed a subcontract for the exchange of $692,000 from UC Davis to USGS. The California Water Science Center (CAWSC) of USGS suballocated $86,000 from the $692,000 to the USGS Western Region office in Menlo Park on 8/7/06 for Dr. Carol Kendall’s group for isotope analyses and interpretation.
Bergamaschi, B.A., Fram, M.S., Fujii, R., Aiken, G.R., Kendall, C., and Silva, S.R., 2000, Trihalomethanes formed from natural organic isolates: using isotopic and compositional data to help understand sources, in Natural organic matter and disinfection by-products, characterization and control in drinking water, Barrett, S.E., Krasner, S.W., and Amy, G.L., editors, ACS Symposium Series 761, p. 206-222.
Bergamaschi, B.A., Kalve, E., Guenther, L., Mendez, G.O., and Belitz, K., 2005, An assessment of optical properties of dissolved organic material as quantitative source indicators in the Santa Ana River Basin, Southern California: USGS Scientific Investigations Report 2005-5152, 38 p.
Bird, S.M., Fram, M.S., and Crepeau, K.L., 2003, Method of analysis by the U.S. Geological Survey California District Sacramento Laboratory—Determination of dissolved organic carbon in water by high temperature catalytic oxidation, method validation, and quality-control practices: USGS Open-File Report 03-366, 14 p.
Burow, K.R., Stork, S.V., and Dubrovsky, N.M., 1998, Nitrate and pesticides in ground water in the eastern San Joaquin Valley, California: occurrence and trends: USGS Water-Resources Investigations Report 98-4040A, 33 p.
Capel, P.D., McCarthy, K.A., and Barbash, J.E., 2008, National, holistic, watershed-scale approach to understand the sources, transport, and fate of agricultural chemicals: Journal of Environmental Quality, vol. 37, pp. 983-993.
Constantz, J., and Thomas, C.L., 1996, The use of streambed temperature profiles to estimate the depth, duration, and rate of percolation beneath arroyos: Water Resources Research, vol. 32, no. 12, pp. 3597-3602.
Essaid, H.I., Zamora, C., McCarthy, K.A., Vogel, J.R., and Wilson, J.T., 2008, Using heat to characterize streambed water flux variability in four stream reaches: Journal of Environmental Quality, vol. 37, pp. 1010-1023.
Gronberg, J.M., Dubrovsky, N.M., Kratzer, C.R., Domagalski, J.L., Brown, L.R., and Burow, K.R., 1998, Environmental setting of the San Joaquin-Tulare Basins, California: USGS Water-Resources Investigations Report 97-4205, 45 p.
Gronberg, J.M., Kratzer, C.R., Burow, K.R., Domagalski, J.L., and Phillips, S.P., 2004, Water-quality assessment of the San Joaquin-Tulare Basins--entering a new decade: U.S. Geological Survey Fact Sheet 2004-3012, 6 p.
Harvey, F.E., Lee, D.R., Rudolph, D.L., and Frape, S.K., 1997, Locating groundwater discharge in large lakes using bottom sediment electrical conductivity mapping: Water Resources Research, vol. 33, no. 11, p. 2609-2615.
Kendall, C. (1998) Tracing nitrogen sources and cycling in catchments. In: C. Kendall. and J.J. McDonnell, (eds.) “Isotope Tracers in Catchment Hydrology,”. Elsevier Science., p. 519 – 576.
Kratzer, C.R., and Shelton, J.L., 1998, Water quality assessment of the San Joaquin-Tulare basins, California: analysis of available data on nutrients and suspended sediment in surface water, 1972-1990: USGS Professional Paper 1587, 92 p.
Kratzer, C.R., Dileanis, P.D., Zamora, C., Silva, S.R., Kendall, C., Bergamaschi, B.A., and Dahlgren, R.A., 2004, Sources and transport of nutrients, organic carbon, and chlorophyll-a in the San Joaquin River upstream of Vernalis, California during summer and fall, 2000 and 2001: USGS Water-Resources Investigations Report 03-4127, 113 p.
Lee, D.R., 1985, Method for locating sediment anomalies in lakebeds that can be caused by groundwater flow: Journal of Hydrology, vol. 79, p. 187-193.
Phillips, S.P., Beard, Sherrill, and Gilliom, R.J., 1991, Quantity and quality of ground-water inflow to the San Joaquin River, California: USGS Water-Resources Investigations Report 91-4019, 64 p.
Puckett, L.J., Zamora, C., Essaid, H., Wilson, J.T., Johnson, H.M., Brayton, M.J., and Vogel, J.R., 2008, Transport and fate of nitrate at the ground-water/surface-water interface: Journal of Environmental Quality, vol. 37, pp. 1034-1050.
U.S. Environmental Protection Agency, 2000, Proceedings of the ground-water/surface-water interactions workshop: sponsored by USEPA’s Office of Solid Waste and Emergency Response, January 1999 in Denver, CO (“sediment probes” or “drag probes” discussed as methods of qualitatively determining ground water “hot spots” in papers by David R. Lee p. 35-38; Thomas C. Winter and Joseph Dlugosz p. 46-53; and Allen Burton and Ned Black p. 54-57). Report available on-line at: http://www.clu-in.org/s.focus/c/pub/i/600/
Wagner, R.J., Mattraw, H.C., Ritz, G.F., and Smith, B.A., 2000, Guidelines and standard procedures for continuous water-quality monitors: site selection, field operation, calibration, record computation, and reporting: USGS Water-resources Investigations Report 00-4252, 53 p.
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