Dubrovsky, N.M., 1991, National Water Quality Assessment Program -- The San Joaquin-Tulare Basins: U.S. Geological Survey Open-File Report 91-153, 2 p. (Water Fact Sheet)

Dubrovsky, N.M., S.J. Deverel, and R.J. Gilliom, 1993, Multiscale approach to regional ground-water quality assessment: Selenium in the San Joaquin Valley, California, in W.M. Alley, ed., Regional Ground-Water Quality, Van Nostrand Reinhold, p. 537-562

Gronberg, J.M., Kratzer, C.R., Burow, K.R., Domagalski, J.L., 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.

Brown, L.R., 1997, Concentrations of chlorinated organic compounds in biota and bed sediment in streams of the San Joaquin Valley, California: Archives of Environmental Contamination and Toxicology, v.33, no. 4, p. 357-368.

Brown, L.R., 1998, Concentrations of chlorinated organic compounds in biota and bed sediment in streams of the lower San Joaquin River drainages, California: U.S. Geological Survey Open-File Report 98-171 22 p.

Brown, L.R., 2004, Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides in the San Joaquin River Basin, California, During Summer Conditions, 1994 and 2001: U.S. Geological Survey Scientific Investigations Report 2004-5083 61p.

Domagalski, J.L., 1993, Pesticides detected in the San Joaquin River Basin, California -- Results of an intensive fixed-station sampling design developed for the National Water Quality Assessment Program (abs.): EOS, Transactions of the American Geophysical Union, Spring Meeting Supplement, v. 74, no.16, p. 129.

Domagalski, J.L., and Dubrovsky, N.M., 1994, Inputs of the dormant orchard pesticide, diazinon, to the San Joaquin River, California, in Sorenson, S.K., ed., Proceedings abstracts of the American Water Resources Association's symposium on the National Water Quality Assessment (NAWQA) Program -- November 7-9, 1994, Chicago, Illinois: U.S. Geological Survey Open-File Report 94-397, p. 8.

Domagalski, J.L., 1996, Occurrence of dicofol in the San Joaquin River, California : Bulletin of Environmental Contamination and Toxicology, v. 57, p. 284-291.

Domagalski, J.L., 1997, Results of a prototype surface water network design for pesticides developed for the San Joaquin River Basin, California: Journal of Hydrology, v. 192, p. 33-50.

Domagalski, J.L., Dubrovsky, N.M., and Kratzer, C.R., 1997, Pesticides in the San Joaquin River, California: Inputs from dormant sprayed orchards: Journal of Environmental Quality, v. 26, no. 2, p. 454-465.

Domagalski, J.L., Ator, S., Coupe, R., McCarthy, K., Lampe, D., Sandstrom, M., and Baker, N., 2008, Comparative study of transport processes of nitrogen, Phosphorus, and herbicides to streams in five agricultural basins, USA: Journal of Environmental Quality 37:1158-1169.

Dubrovsky, N.M., and Domagalski, J.L., 1993, Pesticides detected in the San Joaquin River basin, California: Analysis of existing data and design of monitoring network (abs. ): EOS, Transactions of the American Geophysical Union, Spring Meeting Supplement, v. 74, no. 16, p. 134-135.

Dubrovsky, N.M., Domagalski, J.L., Gronberg, J.M., Kratzer, C.R., Kuivila, K.M., and Panshin, S.Y., 1997, Pesticide occurrence as a function of landuse, application, and hydrology, San Joaquin River, California : Society of Environmental Toxicology and Chemistry, SETAC 17th Annual Meeting, Washington, D.C., November 17-21, 1996, Abstract Book, p. 69.

Dubrovsky, N.M., Kratzer, C.R., Panshin, S.Y., Gronberg, J.M., and Kuivila, K.M., 2000, Pesticide transport in the San Joaquin River Basin: In: Agrochemical Fate and Movement, ACS Symposium Series 751 (Edited by T.R. Steinhamer, L.J. Ross, and T.D. Spittler), pp. 306-322.

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 37:1010-1023.

Kinsey, W.B.. Johnson, M.V., and Gronberg J.M., 2005, Data on Dissolved Pesticides and Volatile Organic Compounds in Surface and Ground Water in the San Joaquin-Tulare Basins, California: U.S. Geological Survey Data Series Report DS-107, p. 372.

Knifong, D.L., and Gronberg, J.M., 1994, Basic fixed site selection and monitoring, San Joaquin-Tulare Basins: Palm Springs, California, ESRI User Conference, May 23-27, 1994, Poster.

Kratzer, C.R., 1994, Nitrate in surface water in the San Joaquin Valley drainage basin, California -- A retrospective assessment (abs.), in Marston, R.A., and Hasfurther, V.R., eds., Effects of human-induced changes on hydrologic systems: American Water Resources Association Summer Symposium, Jackson Hole, Wyoming, June 26-29, Proceedings, p. 1164.

Kratzer, C.R., 1994, An assessment of the increasing nitrate trend in the lower San Joaquin River, California, in Sorenson, S.K., ed., Proceedings abstracts of the American Water Resources Association's symposium on the National Water Quality Assessment (NAWQA) Program -- November 7-9, 1994, Chicago, Illinois: U.S. Geological Survey Open- File Report 94-397, p. 5.

Kratzer, C.R., 1996, Transport of sediment-bound organochlorine pesticides to San Joaquin River, California (abs.): American Water Resources Association, 32nd Annual Conference and Symposium, Ft. Lauderdale, Florida, September 22-26, 1996, oral presentation.

Kratzer, C.R., 1998, Pesticides in storm runoff from agricultural and urban areas in the Tuolumne River Basin in the vicinity of Modesto, California: U.S. Geological Survey Water-Resources Investigations Reports 98-4017, 17 p.

Kratzer, C.R., 1999, Transport of diazinon in the San Joaquin River Basin, California: Journal of the American Water Resources Association, v. 35, no. 2, p. 379-395.

Kratzer, C.R., 1999, Transport of sediment-bound organochlorine pesticides to the San Joaquin River, California: Journal of the American Water Resources Association, v. 35, no. 4, p. 957-981.

Kratzer, C.R., and Biagtan, R.N., 1997, Determination of traveltimes in the Lower San Joaquin River Basin, California, from dye-tracer studies during 1994-1995: U.S. Geological Survey Water Resources Investigations Report 97-4018, 20p.

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: U.S. Geological Survey Professional Paper 1587, 92 p.

Kratzer, C.R., and Dahlgren, R.A., 2006, Investigations of nitrate in the lower San Joaquin River, California: California Plant and Soil Conference Proceedings, CA Chapter of American Society of Agronomy, pp. 159-165.

Panshin, S.Y., Domagalski, J.L., and Dubrovsky, N.M., 1994, Pesticide concentrations in surface water as a function of agricultural land use in five small watersheds, western San Joaquin Valley, California (abs.): EOS, Transactions of the American Geophysical Union, v. 75, no. 44, Supplement, p. 246.

Panshin, S.Y., Dubrovsky, N.M., Gronberg, J.M., and Domagalski, J.L., 1998, Occurrence and distribution of dissolved pesticides in the San Joaquin Basin, California, U.S. Geological Survey Water-Resources Investigations 98-4032, p. 88.

Panshin, S.Y., Kratzer, C.R., Gronberg, J.M., Dubrovsky, N.M., Domagalski, J.L., 1995, Diazinon concentrations in surface water of the lower San Joaquin Basin, California (abs.): Society of Environmental Toxicology and Chemistry abstract book, Second SETAC World Congress (16th annual meeting), Global Environmental Protection: Science, Politics, and Common Sense, Vancouver, British Columbia, Canada, p. 157.

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 37:1034-1050.

Saleh, D.K., 2006, Using the Soil and Water Assessment Tool (SWAT) to simulate runoff in Mustang Creek Basin, California: M.S. Thesis, California State University, Sacramento.

Vogel, J.R., Majewski, M.S., and Capel, P.D., 2008, Pesticides in rain in four agricultural watersheds in the United States: Journal of Environmental Quality 37:1101-1115.

Zamora, C., 2006, Estimating rates of exchange across the sediment-water interface in the Lower Merced River, CA: M.S. Thesis, California State University, Sacramento.

Zamora, C., 2007, Estimating water fluxes across the sediment-water interface in the Lower Merced River, CA: U.S. Geological Survey Scientific Investigations Report 2007-5216.

Bexfield, L.M., 2008, Decadal-scale changes of pesticides in ground water of the United States, 1993-2003: Journal of Environmental Quality 37:S-226-S-239.

Brown, C.J., Jurgens, B.C., Katz, B.G., Landon, M.K., and Eberts, S.M., 2007, Arsenic and uranium in four aquifer settings: occurrence, distribution, and mechanisms for transport to supply wells: 2007 NGWA Naturally Occurring Contaminants Conference: Arsenic, Radium, Radon, Uranium, March 22-23, 2007, Charleston, South Carolina.

Burow, K.R., Dubrovsky, N.M., and Panshin, S.Y., 1995, Evaluation of chemical and physical processes controlling DBCP fate and transport in the western San Joaquin Valley, California, (abs.): EOS, Transactions of the American Geophysical Union, v. 76, no. 46, Supplement, p. 186-187.

Burow, K.R., Panshin, S.Y., Dubrovsky, N.M., VanBrocklin, David, and Fogg, G.E., 1999, Evaluation of processes affecting 1,2-Dibromo-3-Chloropropane (DBCP) concentrations in ground water in the eastern San Joaquin Valley, California: Analysis of chemical data and ground-water flow and transport simulations: U.S. Geological Survey Water-Resources Investigations Report 99-4059, 57p.

Burow, K.R., Shelton, J.L., and Dubrovsky, N.M., 1998, Occurrence of nitrate and pesticides in ground water beneath three agricultural land-use settings in the eastern San Joaquin Valley, California, 1993-1995: U.S. Geological Survey Water-Resources Investigations Reports 97-4284, 51 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: U.S. Geological Survey Water-Resources Investigations Report98-4040a, 33 p.

Burow, K.R., Weissmann, G.S., Miller, R.D., and Placzek, Gary, 1997, Hydrogeologic facies characterization of an alluvial fan near Fresno, California, using geophysical techniques: U.S. Geological Survey Open-File Report 97-46, 15 p.

Burow, K.R., Shelton, Jennifer L., Hevesi, Joseph A., Weissmann, Gary S., 2004, Hydrogeologic characterization of the Modesto Area, San Joaquin Valley, California: U.S. Geological Survey Scientific Investigations Report 2004-5232, 62 p.

Burow, K.R., Jurgens, B.C., Kauffman, L.J., Phillips, S.P., Dalgish, B.A., and Shelton, J.L., 2008, Simulations of ground-water flow and particle pathline analysis in the zone of contribution of a public-supply well in Modesto, eastern San Joaquin Valley, California: U.S. Geological Survey Scientific Investigations Report 2008-5035, 41p.

Burow, K.R. and Green, C.T., 2008, Spatial and Temporal Trends in Nitrate Concentration In the Eastern San Joaquin Valley Regional Aquifer and Implications for Nitrogen Fertilizer Management: California Plant and Soil Conference: Conservation of Agricultural Resources, February 5 & 6, 2008, Visalia, California.

Burow, K.R., Shelton, J.L., and Dubrovsky, N.M., 2008, Regional nitrate and pesticide trends in ground water in the eastern San Joaquin Valley, California: Journal of Environmental Quality 37:S-249-S-263.

Chapelle, F.H., McMahon, P.B., Dubrovsky, N.M., Fujii, R.F., Oaksford, E.T., and Vroblesky, D.A., 1995, Deducing the distribution of terminal electron-accepting processes in hydrologically diverse groundwater systems: Water Resources Research,Vol. 31, No. 2, p. 359-371.

Domagalski, J.L., Xinquan, Zhou, Chao, Lin, Deguo, Zhi, Chi, F.L., Kaitai, Xu, Ying, Lu, Yang, Luo, Shide, Liu, Dewen, Liu, Yong, Guo, Qi, Tian, Jing, Liu, Weidong, Yu, Shedlock, Robert, Knifong, Donna, 2001, Comparative water-quality assessment of the Hai He River Basin in the People's Republic of China and three similar areas in the United States: U.S. Geological Survey Professional Paper 1647, 58 p.

Dubrovsky, N.M., Burow, K.R., and Gronberg, J.M., 1995, Effects of two contrasting agricultural land uses on shallow ground water quality in the San Joaquin Valley, California -- Design and preliminary interpretation: International Union Geodesy and Geophysics, XXI General Assembly, Boulder, Colo., July 2-14, Abstracts-Week A, p. 205.

Dubrovsky, N.M., Burow, K.R., and Gronberg, J.M., 1995, Effects of two contrasting agricultural land uses on shallow ground water quality in the San Joaquin Valley, California -- Design and preliminary interpretation, in Wagner, B.J., Illangasekare, T.H., and Jensen, K.H., eds., Models for assessing and monitoring groundwater quality: Wallingford, Oxfordshire, U.K., International Association of Hydrological Sciences, publication 227, proceedings, p.49-58.

Fisher, L.H., and Healy, R.W., 2008, Water movement within the unsaturated zone in four agricultural areas of the United States: Journal of Environmental Quality 37:1051-1063.

Green, C.T., Fisher, L.H., and Bekins, B.A., 2008, Nitrogen fluxes through unsaturated zones in five agricultural settings across the United States: Journal of Environmental Quality 37:1073-1085.

Green, C.T., Puckett, L.J., Bohlke, J.K., Bekins, B.A., Phillips, S.P., Kaufmann, L.J., Denver, J.M., and Johnson, H.M., 2008, Limited occurrence of denitrification in four shallow aquifers in agricultural areas of the United States: Journal of Environmental Quality 37:994-1009.

Gronberg, J.M., and Knifong, D.L., 1994, Use of Geographic Information System in analyzing effects of land use on ground-water quality, San Joaquin-Tulare Basins, California, in Marston, R.A., and Hasfurther, V.R., eds., Proceedings -- Effects human-induced changes on hydrologic systems: American Water Resources Association, 1994, Annual Summer Symposium, Jackson Hole, Wyoming, June 26-29, 1994, Poster, p. 103.

Hancock, T.C., Sandstrom, M.W., Vogel, J.R., Webb, R.M.T., Bayless, E.R., and Barbash, J.E., 2008, Pesticide fate and transport throughout unsaturated zones in five agricultural settings, USA: Journal of Environmental Quality 37:1086-1100.

Jurgens, B.C., Burow, K.R., Dalgish, B.A., and Shelton, J.L., 2008, Hydrogeology, water chemistry, and factors affecting the transport of contaminants in the zone of contribution of a public-supply well in Modesto, Eastern San Joaquin Valley, California: U.S. Geological Survey Scientific Investigations Report 2008-5156, 78p.

Landon, M.K., Eberts, S.M., Jurgens, B.C., Katz, B.G., Burow, K.R., Crandall, C.A., Brown, C.J., and Starn J.J., 2006, Knowledge of Where and How Contamination- Susceptible Water Enters Public-Supply Wells Can Be Used To Improve Monitoring Strategies and Protection Plans: Ground Water Protection Council Annual Forum 2006, Sept. 30 – Oct. 4, 2006, Miami Beach, FL, 15 p.

McMahon, P. B., Bohlke, J. K., Kauffman, L. J., Kipp, K. L., Landon, M. K., Crandall, C. A., Burow, K. R., and Brown, C. J., 2008, Source and transport controls on the movement of nitrate to public supply wells in selected principal aquifers of the United States , Water Resources Research, 44, W04401, doi:10.1029/2007WR006252.

McMahon, P.B., Burow, K.R., Kauffman, L.J., Eberts, S.M., Böhlke, J.K., and Gurdak, J.J., 2008, Simulated response of water quality in public supply wells to land use change, Water Resources Research, Volume 44, W00A06, doi:10.1029/2007WR006731.

Panshin, S.Y., 1997, Determining concentrations of 2-bromoally alcohol and dibromopropene in ground water using quantitative methods: U.S. Geological Survey Open-File Report 97-43, 7 p.

Phillips, S.P., Burow, K.R., Rewis, D.L., Shelton, J., and Jurgens, B., 2007, Hydrogeologic setting and ground- water flow simulations of the San Joaquin Valley regional study area, California; Section 4 of Paschke, Suzanne S., ed., 2007, Hydrogeologic settings and ground-water flow simulations for regional studies of the transport of anthropogenic and natural contaminants to public-supply wells—studies begun in 2001 : U.S. Geological Survey Professional Paper 1737-A, 244p.

Phillips, S.P., Green, C.T., Burow, K.R., Shelton, J.L., and Rewis, D.L., 2007, Simulation of Multiscale Ground-Water Flow in Part of the Northeastern San Joaquin Valley, California: U.S. Geological Survey Scientific Investigations Report 2007–5009, 55p.

Rosen, M.R., and Lapham, W.W., 2008, Introduction to the U.S. Geological Survey National Water-Quality Assessment (NAWQA) of ground-water trends and comparison to other national programs: Journal of Environmental Quality 37:S-190-S-198.

Rosen, M.R., Voss, F.D., and Arufe, J.A., 2008, Evaluation of intra-annual variation in U.S. Geological Survey national water quality assessment ground water quality data: Journal of Environmental Quality 37:S-199-S-208.

Rupert, M.G., 2008, Decadal-scale changes of nitrate in ground water of the United States, 1988-2004: Journal of Environmental Quality 37:S-240-S-248.

Spurlock, F., Burow, K., Dubrovsky, N., 2000, Chlorofluorocarbon dating of herbicide-containing well waters in Fresno and Tulare counties, California: Journal of Environmental Quality, v. 29, no. 2, p. 474-483.

Brown, L.R., 1992, Biological and data management aspects of the National Water Quality Assessment Program in the San Joaquin-Tulare Basins, California(abs.): California-Nevada Chapter of the American Fisheries Society, 27th Annual Conference, Redding, California, February 6-8, Program, p. 15-16.

Brown, L.R., 1994, Responses of fish and macroinvertebrate communities to variations in habitat and water quality in streams of the San Joaquin Valley, California, in Sorenson, S.K., ed., Proceedings abstracts of the American Water Resources Association's symposium on the National Water Quality Assessment (NAWQA) Program -- November 7-9, 1994, Chicago, Illinois: U.S. Geological Survey Open-File Report 94-397, p. 20.

Brown, L.R., 1995, Native and introduced stream fishes of the San Joaquin Valley floor -- Their relation to quality of water and habitat: American Fisheries Society, California-Nevada Chapter, Consensus building in resource management, Napa, California, February 3-4, Program and Abstracts, p. 13.

Brown, L.R., 1996, Annual and spatial variability of fish assemblages at locations in the lower San Joaquin River drainage (abs): American Fisheries Society, 31st Annual Conference, California-Nevada Chapter, Aquatic species loss and imperilment -- Perspectives for our profession, Ventura, Calif., p. 20.

Brown, L.R., 1996, Aquatic Biology of the San Joaquin-Tulare Basins, California: Analysis of Available Data Through 1992, Water-Supply Paper 2471, 89 p.

Brown, L.R., 2000, Fish communities and their associations with environmental variables, lower San Joaquin River drainage, California: Environmental Biology of Fishes 57:251-269.

Brown, L.R., and May, J.T., 2000, Benthic macroinvertebrate assemblages and their relations with environmental variables in the Sacramento and San Joaquin Drainages, California: U.S. Geological Survey Water-Resources Investigations Report 00-4125, 25 p.

Brown, L.R., and May, J.T., 2000, Macroinvertebrate assemblages on woody debris and their relations with environmental variables in the lower Sacramento and San Joaquin river drainages, California: Environmental Monitoring and Assessment 64:311-329.

Leland, H.V., L.R. Brown, and D.K. Mueller, 2001, Distribution of algae in the San Joaquin River, California, in relation to nutrient supply, salinity, and other environmental factors: Freshwater Biology 46:1139-1167.

Brown, L.R., 2004, Periphyton and Macroinvertebrate Communities at Five Sites in the San Joaquin River Basin, California, during June and September, 2001: U.S. Geological Survey Scientific Investigations Report 2004-5098 47p.

Konrad, C.P., Brasher, A.M.D., and May, J.T., 2008, Assessing streamflow characteristics as limiting factors on benthic invertebrate assemblages in streams across the western United States: Freshwater Biology, vol. 53, issue 10, pp. 1983-1998.

May, J.T., and Brown, L.R., 2001, Chinese Mitten Crab Surveys of San Joaquin River Basin and Suisun Marsh, California, 2000: U.S. Geological Survey Open-File Report 01-396, 24 p.

Brown, L.R., Kratzer, C.R., and Dubrovsky, N.M., 1996, Integrating chemical, water quality, and habitat data with fish assemblage data from the San Joaquin River drainage, in From cumulative impacts towards sustainable solutions -- Critical methodologies for the study of ecosystem health: Davis, California, Center for Ecological Health Research, Agenda and Abstracts, p. 4.

Brown L.R., Kratzer, C.R., and Dubrovsky, N.M., 1999, Integrating chemical, water quality, habitat, and fish assemblage data from the San Joaquin River drainage, California, in, K.M. Scow, G.E. Fogg, D.E. Hinton, and M.L. Johnson (eds.), Integrated assessment of ecosystem health, Lewis Publishers, Boca Raton, FL, p. 25-62.

Brown, L.R. and Short, T.M., 1999, Biological, Habitat and Water Quality Conditions in the Upper Merced River Drainage, Yosemite National Park, California, 1993-1996: U.S. Geological Survey Water-Resources Investigations Report 99-4088, 56 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 37:983-993.

Domagalski, J.L., 1997, Pesticides in surface and ground water of the San Joaquin-Tulare Basins, California: Analysis of Available Data, 1966 through 1992: U.S. Geological Survey Water-Supply Paper 2468, 74 p.

Domagalski , J.L., Phillips, S.P., Bayless, E.R., Zamora, C.M., Kendall, Carol, Wildman, R.A., and Hering, J.G., 2008, Influences of the unsaturated, saturated, and riparian zones on the transport of nitrate near the Merced River, California, USA: Hydrogeology Journal 16: 675-690.

Dubrovsky, N.M., Kratzer, C.R., Brown, L.R., Gronberg, J.M., and Burow, K.R., 1998, Water quality in the San Joaquin-Tulare Basins, California, 1992-95: U.S. Geological Survey Circular 1159, 38 p.

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: U.S. Geological Survey Water-Resources Investigations Report 97-4205, 45 p.

Gronberg, J.M., and Kratzer, C.R., 2006, Environmental setting of the lower Merced River Basin, California: U.S. Geological Survey Scientific Investigations Report 2006-5152, 27 p.

Pereira, W.E., Domagalski, J.L., Hostettler, F.D., Brown, L.R., and Rapp, J.B., 1996, Occurrence and accumulation of pesticides and organic contaminants in river sediment, water, and clam tissues from the San Joaquin River and tributaries, California: Environmental Toxicology and Chemistry, v. 15, no. 2, p. 172-180.

Steele, G.V., Johnson, H.M., Sandstrom, M.W., Capel, P.D., and Barbash, J.E., 2008, Occurrence and fate of pesticides in four contrasting agricultural settings in the United States: Journal of Environmental Quality 37:1116-1132.