68) Stieglitz, T. C., J. F. Clark, and G. Hancock (2013) The Mangrove Pump: rapid tidal Flushing of Animal Burrows in Mangrove Forests, a major driver of Land-Ocean Solute Fluxes in the Tropics. Geochimica et Cosmochimica Acta, 102, 12-22,

67) Manning, A. H., J. F. Clark, S. H. Diaz, L. K. Rademacher, S. Earman, L. N Plummer (2012) Evolution of groundwater age in a mountain watershed over a period of thirteen years. Journal of Hydrology, 460, 13-28, doi:10.1016/j.jhydrol.2012.06.030.

66) Fisher, A. T., J. Cowen, C. G. Wheat, and J. F. Clark (2011), Preparation and injection of fluid tracers during IODP Expedition 327, eastern flank of Juan de Fuca Ridge in Proc. IODP 327, edited by A. T. Fisher, T. Tsuji and K. Petronotis. doi:10.2204/iodp.proc.327.108.2011, Integrated Ocean Drilling Program Management International, Inc., Tokyo.
65) Kline, K. R., D. M. Mackay, L. Rastegarzadeh, Y. M. Nelson, J. F. Clark (2011) In-Situ Rates of Ethanol Biodegradation in a Sulfate-Reducing Aquifer Determined using Single Well Push-Pull Tests. Ground Water Monitoring and Remediation, 31, 103-110 doi:10.1111/j1745-6592.2011.01347.x.

64) Morrissey, S. K., J. F. Clark, M Bennett, E. Richardson, and M. Stute (2010) Groundwater reorganization in the Floridan aquifer following Holocene sea-level rise. Nature Geoscience, 3, 683-687, doi:10.1038/NGEO956.
63) Clark, J. F., L. Washburn, and K. Schwager (2010) Variability of gas composition and flux intensity in natural marine hydrocarbon seeps. Geo-Marine Letters, 30, 379-388, doi:10.1007/s00367-009-0167-1.

62) MacIntyre, S., J. F. Clark, R. Jellison (2009) Turbulent mixing induced by nonlinear waves in Mono Lake. Limnology and Oceanography, 54, 2255-2272.

61) Rueda, F. J, S. G. Schladow and J. F. Clark (2008) Mechanisms of contaminant transport in a multi-basin lake. Ecological Applications. 18 Supplement, A72-A87.
60) Schladow, S. G. and J. F. Clark (2008) Use of Tracers to Quantify Subsurface Flow Through a Mining Pit. Ecological Applications, 18 Supplement, A55-A71.
59) Schmieder, P. J., D. T. Ho, P. Schlosser, J. F. Clark, and S. G. Schladow (2008) An SF6 tracer study of the flow dynamics in the Stockton Deep Water Ship Channel: Implications for dissolved oxygen dynamics. Estuaries and Coasts, 31, 1038-1051, doi:10.1007/s12237-008-9093-0.
58) Meillier, L. H. Loáiciga, and J. F. Clark (2008) Ground water dating and flow-model calibration in the Kern Water Bank, California. Journal of Hydrologic Engineering, ASCE, 13, 1029-1038.
57) McDermott, J. A., D. Avisar, T. Johnson, and J. F. Clark (2008) Groundwater travel times near spreading ponds: Inferences from geochemical and physical approaches. Journal of Hydrologic Engineering, ASCE, 13, 1021-1028.
56) Blumhagen, E. D. and J. F. Clark (2008) Carbon sources and signals through time in an alpine groundwater basin, Sagehen California. Applied Geochemistry, 23, 2284-2291, doi:10.1016/j.apgeochem.2008.03.010.

55) Duffy, M., F. S. Kinnaman, D. L. Valentine, E. A. Keller, and J. F. Clark (2007) Gaseous Hydrocarbon Fluxes from Natural Seeps in the Upper Ojai Valley, CA. Environmental Geosciences, 14, 197-207.
54) Mau, S., D. L. Valentine, J. F. Clark, J. Reed, R. Camilli, and L. Washburn (2007) Dissolved methane distributions and air-sea flux in the plume of a massive seep field, Coal Oil Point, California. Geophysical Research Letter, 34, L22603, doi:10.1029/2007GL031344.
53) Clark, J. F. (2007) Tracing Recharge Water from Spreading Ponds: A Decade of Studies. In: Management of Aquifer Recharge for Sustainability, ed. Fox, P., Acacia, Phoenix, p. 285-295.
52) Clark, J. F. and T. Stieglitz (2007) 2.2.2 Isotope and Tracer Techniques. In: Submarine Groundwater, ed. Zektser, I., L. G. Everett, and R. G. Dzhamalov, CRC Press, p. 110-117.

51) Clark, J. F. and G. B. Hudson (2006) Excess air: A new tracer for artificially recharged surface water. In: Recharge Systems for Protecting and Enhancing Groundwater Resources, IHP-VI, Series on Groundwater No. 13, UNESCO, p. 342-347. Available at
50) Avisar, D., J. F. Clark, J. D. McDermott, and G. B. Hudson (2006) A comparison of three methods for determining travel times near a large artificial recharge facility. In: Recharge Systems for Protecting and Enhancing Groundwater Resources, IHP-VI, Series on Groundwater No. 13, UNESCO, 247-252. Available at
49) Clark, J. F. (2006) Managing aquifer recharge: How can isotope hydrology help? Water & Environment News, Newsletter of the Isotope Hydrology Section, International Atomic Energy Agency, 21, 10.
48) Cook, P. G., S. Lamontagne, D. Berhane, J. F. Clark (2006) Quantifying groundwater discharge to Cockburn River, southeastern Australia, using dissolved gas tracers 222Rn and SF6. Water Resources Research, 42, W10411, doi:10.1029/2006WR004921.
47) Leifer, I., B. P. Luyendyk, J. R. Boles, J. F. Clark (2006) Natural marine seepage blowout: Contribution to atmospheric methane. Global Biogeochemical Cycles, 20, GB3008 10.1029/2005GB002668.

46) Clark, J. F., K. Schwager, and L. Washburn (2005) Variability of gas composition and flux intensity in natural marine hydrocarbon seeps. New Energy Development and Technology (EDT) Working Paper, 008, UCEI, 15 p.
45) Avisar, D. and J. F. Clark (2005) Evaluating travel times beneath an artificial recharge pond using sulfur hexafluoride. Environmental and Engineering Geoscience, 11, 309-317.
44) Luyendyk, B. P., J. P. Kennett, and J. F. Clark (2005) Hypothesis for increased atmospheric methane input from hydrocarbon seeps on exposed continental shelves during glacial low sea level. Marine and Petroleum Geology, 22, 591-596.
43) Washburn, L., J. F. Clark, and P. Kyriakidis (2005) The spatial scales, distribution, and intensity of natural marine hydrocarbon seeps near Coal Oil Point, California. Marine and Petroleum Geology, 22, 569-578.
42) Clark, J. F., G. B. Hudson, and D. Avisar (2005) Gas transport below artificial recharge ponds: Insights from dissolved noble gases and a dual gas (SF6 and 3He) tracer experiment. Environmental Science and Technology, 39, 3939-3945.
41) Rademacher, L. K., J. F. Clark, D. W. Clow, G. B. Hudson (2005) Old groundwater influence on stream hydrochemistry and catchment response in a small Sierra Nevada catchment: Sagehen Creek, California. Water Resources Research, 41, W02004, doi:10.1029/2003WR002805.

40) Leifer, I., J. R. Boles, B. P. Luyendyk and J. F. Clark (2004) Transient discharges from marine hydrocarbon seeps: Spatial and temporal variability. Environmental Geology, 46, 1038-1052.
39) Cook, P. G., T. Stieglitz, J. Clark (2004) Groundwater discharge from the Burdekin Floodplain aquifer, North Queensland, CSIRO Land and Water Technical Report N. 26/04, 118 p.
38) Clark, J. F., G. B. Hudson, M. L. Davisson, G. Woodside, and R. Herndon (2004) Geochemical imaging of flow near an artificial recharge facility, Orange County, CA. Ground Water, 42, 167-174.

37) Leifer, I., J. F. Clark, B. Luyendyk, and D. Valentine (2003) Identifying future directions for subsurface hydrocarbon migration research. EOS, 84, 364-371.
36) Clark, J. F., I. Leifer, L. Washburn, B. P. Luyendyk (2003) Compositional changes in natural gas bubble plumes: Observations from the Coal Oil Point Seep Field. Geo-Marine Letters, 23, 187-193.
35) Fram, M. S., B. A. Bergamaschi, K. D. Goodwin, R. Fujii, and J. F. Clark (2003) Processes affecting the trihalomethane concentrations associated with the third injection, storage, and recovery test at Lancaster, Antelope Valley, California, March 1998 through April 1999. Water-Resources Investigations Report 03-4062, 72 p.
34) Avisar, D. and J. F. Clark (2003) A gas tracer study in the El-Rio spreading ponds, Ventura County, California. Proceedings of the 11th Biennial Symposium on Groundwater Recharge.
33) Clark. J. F. (2003) Application of geochemical tracers for flow characterization near artificial recharge operations. Proceedings of the 11th Biennial Symposium on Groundwater Recharge.
32) Thomas, J. M., M. Stute, J. F. Clark, G. B. Hudson (2003) Noble gas loss may indicate groundwater flow across flow barriers in southern Nevada. Environmental Geology, 43, 568-579.
31) Rademacher, L. K., J. F. Clark, and J. R. Boles (2003) Groundwater residence times and flow paths in fractured rock determined using environmental tracers in the Mission Tunnel; Santa Barbara County, California, USA. Environmental Geology, 43, 557-567.

30) Leifer, I. and J. F. Clark (2002) Modeling trace gases in hydrocarbon seep bubbles: Application to marine hydrocarbon seeps in the Santa Barbara Channel. Russian Geology and Geophysics, 47, 572-579. English translation published by the American Geophysical Union.
29) Clark, J. F. (2002) Defining transport near ASR operations using sulfur hexafluoride gas tracer experiments. In: Dillon, P. J. (ed.) Management of Aquifer Recharge for Sustainability, A. A. Balkema, Lissa, 257-260.
28) Aeschbach-Hertig, W., M. Stute, J. F. Clark, R. Reuter, and P. Schlosser, (2002) A paleotemperature record derived from dissolved noble gases in groundwater of the Aquia Aquifer (Maryland, USA). Geochimica et Cosmochimica Acta, 66, 797-817.
27) Rademacher, L. K., J. F. Clark, and G. B. Hudson (2002) Temporal changes in stable isotope composition of spring waters: Implications for recent changes in climate and atmospheric circulation, Geology, 20, 139-142.

26) Boles, J. R., J. F. Clark, I. Leifer, L. Washburn (2001) Temporal variation in natural methane seep rate due to tides, Coal Oil Point area, California. Journal of Geophysical Research, 106, 27,077-27,086.
25) Clark, J. F., G. Woodside, J. D. Gamlin (2001) Tracing groundwater artificially recharged from a river using sulfur hexafluoride, Proceedings of the American Water Resources Association Annual Spring Specialty Conference, 91-96.
24) Rademacher, L. K., J. F. Clark, G. B. Hudson, D. C. Erman, and N. A. Erman (2001) Chemical evolution of shallow groundwater as recorded by springs, Sagehen basin, Nevada County California. Chemical Geology, 179, 37-51.
23) Gamlin, J. D., J. F. Clark, G. Woodside, and R. Herndon (2001) Large-scale tracing of ground water with sulfur hexafluoride. Journal of Environmental Engineering, ASCE, 127, 171-174.
22) Clark, J. F. and G. B. Hudson (2001) Quantifying the flux of hydrothermal fluids into Mono Lake by use of helium isotopes. Limnology and Oceanography, 46, 189-196.

21) Leifer, I., J. F. Clark, and R. F. Chen (2000) Modifications of the local environment by natural marine hydrocarbon seeps. Geophysical Research Letters, 27, 3711-3714.
20) Clark, J. F., Washburn, L., Hornafius, J. S., and Luyendyk, B. P. (2000) Dissolved hydrocarbon flux from natural marine seeps to the southern California Bight. Journal of Geophysical Research, 105, 11,509-11,522.
19) Macfarlane, P. A., Clark, J. F., Davisson, M. L., Hudson, G. B., and Whittemore, D. O. (2000) Late Quaternary recharge determined from chloride in shallow groundwater in central Great Plains. Quaternary Research, 53, 167-174.

18) Quigley, D. C., J. S. Hornafius, B. P. Luyendyk, R. D. Francis, J. F. Clark, and L. Washburn (1999) Decrease in natural marine hydrocarbon seepage near Coal Oil Point, California associated with offshore oil production. Geology, 27, 1047-1050.

17) Clark, J. F, M. L. Davisson, G. B. Hudson, and P. A. Macfarlane (1998) Noble gases, stable isotopes, and radiocarbon as tracers of flow in the Dakota aquifer, Colorado and Kansas. Journal of Hydrology, 211, 151-167.
16) Aeschbach-Hertig, W., P. Schlosser, M. Stute, H. J. Simpson, A. Ludin, and J. F. Clark (1998) A 3H/3He study of groundwater flow in a fractured bedrock aquifer, Ground Water, 36, 661-670.

15) Macfarlane, P. A., J. F. Clark, D. O. Whittemore, M. L. Davisson, and G. B. Hudson (1997) Holocene and late Pleistocene climate conditions in the central Great Plains deduced from noble gases, stable isotopes, Cl, and 36Cl in shallow groundwater. Kansas Geological Survey Open-File-Report #97-77, 28 p.
14) Clark, J. F., M. Stute, P. Schlosser, S. Drenkard, and G. Bonani (1997) An isotope study of the Floridan aquifer in Southeastern Georgia: Implications for groundwater flow and paleoclimate. Water Resources Research, 33, 281-289.

13) Clark, J. F., P. Schlosser, M. Stute, and H. J. Simpson (1996) SF6-3He tracer release experiment: A new method of determining longitudinal dispersion coefficients in large rivers. Environmental Science and Technology, 30, 1527-1532.

12) Clark, J. F., P. Schlosser, H. J. Simpson, M. Stute, R. Wanninkhof, and D. T. Ho (1995) Relationship between gas transfer velocities and wind speeds in the tidal Hudson River determined by the dual tracer technique. In: Air-Water Gas Transfer, eds. Jähne, B. and E. Monahan, Aeon Verlag, Hanau, 785-800.
11) Clark, J. F., W. M. Smethie, Jr., and H. J. Simpson (1995) Chlorofluorocarbons in the Hudson estuary during summer months. Water Resources Research, 31, 2553-2560.
10) Stute, M., M. Forster, H. Frischkorn, A. Serejo, J. F. Clark, P. Schlosser, W. S. Broecker, and G. Bonani (1995) 5° C cooling of tropical Brazil during the last glacial maximum. Science, 269, 379-383.
9) Clark, J. F., H. J. Simpson, R. F. Bopp, and B. Deck (1995) Dissolved oxygen in lower Hudson estuary: 1978-93. Journal of Environmental Engineering, ASCE, 121, 760-763.
8) Stute, M., J. F. Clark, P. Schlosser, W. S. Broecker, and G. Bonani (1995) A high altitude continental paleotemperature record derived from noble gases dissolved in groundwater from the San Juan Basin, New Mexico. Quaternary Research, 43, 209-220.
7) Clark, J. F., P. Schlosser, R. Wanninkhof, H. J. Simpson, W. S. F. Schuster, D. T. Ho (1995) Gas transfer velocities for SF6 and 3He in a small pond at low wind speeds. Geophysical Research Letters, 22, 93-97.

6) Clark, J. F., R. Wanninkhof, P. Schlosser, H. J. Simpson (1994) Gas exchange in the tidal Hudson River using a dual tracer technique. Tellus, 46B, 274-285.

5) Stute, M., J. F. Clark, F. M. Phillips, and D. Elmore (1993) Reconstruction of late glacial climates from the groundwater archive: Cl and 36Cl in the Carrizo aquifer, Texas. Applications of Isotope Techniques in Studying Past and Current Environmental Changes in the Hydrosphere and the Atmosphere, IAEA, Vienna, 259-270.

4) Clark, J. F., H. J. Simpson, W. M. Smethie, Jr., and C. Toles (1992) Gas exchange in a contaminated estuary inferred from chlorofluorocarbons. Geophysical Research Letters, 19, 1133-1136.
3) Stute, M., P. Schlosser, J. F. Clark, and W. S. Broecker (1992) Paleotemperatures in the southwestern United States derived from noble gas measurements in groundwater. Science, 256, 1000-1003.
2) Clark, J. F., H. J. Simpson, R. F. Bopp, and B. Deck (1992) Geochemistry and loading history of phosphate and silicate in the Hudson estuary. Estuarine, Coastal and Shelf Science, 34, 213-233.

1) Clark, J. F. and K. K. Turekian (1990) Time scale of hydrothermal water - rock reactions in Yellowstone National Park based on radium isotopes and radon. Journal of Volcanology and Geothermal Research, 40, 169-180.