* Boynton, W., J.T. Hollibaugh, D. Jay, M. Kemp, J. Kremer, C. Simenstad, S.V. Smith and I. Valiela. 1992. Understanding changes in coastal ecosystems: the Land Margin Ecosystems Program. Eos 73: 481, 484-485.

* Chambers, R. M., J. W. Fourqurean, J. T. Hollibaugh, and S. M. Vink. 1995. Importance of terrestrially-derived particulate phosphorus to phosphorus dynamics in a West Coast Estuary. Estuaries 18: 518-526.

* Chambers, R. M., J. T. Hollibaugh, and S. Vink. 1994. Sulfate reduction and sediment metabolism in Tomales Bay, California. Biogeochemistry 25: 1-18.

* Chambers, R. M., S. V. Smith, and J. T. Hollibaugh. 1994. An ecosystem-level context for tidal exchange studies in salt marshes of Tomales Bay, California, USA. pp. 265-276 In W. J. Mitsch (ed.) Global Wetlands, Old World and New, Elsevier, NY.

* Christensen, S. J. 1995. Benthic flux and pore water models of the upper sediments of Tomales Bay, California. MS thesis, U. Hawaii, 96 pp.

Cole, B. E., S. W. Hager and J. T. Hollibaugh. 1990. Hydrographic, biological and nutrient properties of Tomales Bay, California, March 1985 to May 1986. U.S. Geological Survey Open File Report 90-178.

* Dollar, S. J., S. V. Smith, S. M. Vink, S. Obrebski, and J. T. Hollibaugh. 1991. Annual cycle of benthic nutrient fluxes in Tomales Bay, California, and contribution of the benthos to total ecosystem metabolism. Marine Ecology--Progress Series 79: 115-125.

* Fischer, D. T. 1993. Modeling surface water runoff in the Tomales Bay watershed, Marin County, California. Undergraduate thesis in Geography, Middlebury College, Middlebury, VT, 21 pp.

* Fischer, D. T., S. V. Smith, and R. R. Churchill. 1996. Simulation of a century of runoff across the Tomales watershed, Marin County, California. Journal of Hydrology 186: 253-273.

* Fourqurean, J. W., T. O. Moore, B. Fry, and J. T. Hollibaugh. 1997. Spatial and temporal variation in C:N:P ratios, d ¹⁵N, and d ¹³C of eelgrass Zostera marina as indicators of ecosystem processes, Tomales Bay, California, USA. Marine Ecology—Progress Series 157: 147-157.

* Fourqurean, J. W., K. L. Webb, J. T. Hollibaugh, and S. V. Smith. 1997. Contributions of the plankton community to ecosystem respiration, Tomales Bay, California. Estuarine, Coastal and Shelf Science 44: 493-505.

* Freifelder, R. R., S. V. Smith, and R. H. Bennett. In press. Cows, humans, and hydrology in the nitrogen dynamics of a grazed rural watershed. Journal of Environmental Management.

Friedman, C. S., T. McDowell, J. M. Groff, J. T. Hollibaugh, D. Manzer and R. P. Hedrick. 1988. Presence of Bonamia ostreae among populations of the European flat oyster, Ostrea edulis Linne, in Tomales Bay, California, USA. Journal of Shellfish Research 8: 1033-1037.

Gordon, D. C., P. R. Boudreau, K. H. Mann, J.-E. Ong, W. Silvert, S. V. Smith, G. Wattayakorn, F. Wulff, and T. Yanagi.1996. LOICZ Biogeochemical Modelling Guidelines. LOICZ Reports and Studies No. 5, 96 pp.

* Harvey, J. W., R. M. Chambers, and J. R. Hoelscher. 1995. Preferential flow and segregation of porewater solutes in wetland sediment. Estuaries 18:568-578.

* Hearn, C. J., and J. L. Largier. In press. The summer buoyancy dynamics of a shallow mediterranean estuary and some effects of changing bathymetry; Tomales Bay, California. Estuarine, Coastal and Shelf Science.

* Hearn, C. J., J. L. Largier, S. V. Smith, J. Plant, and J. Rooney. 1997. Effects of changing bathymetry on the summer buoyancy dynamics of a shallow mediterranean estuary: Tomales Bay, California. pp. 243-253. David G. Aubrey and Carl T. Friedrichs (eds.) Buoyancy Effects on Coastal and Estuarine Dynamics. Coastal and Estuarine Studies volume 53, AGU.

* Hollibaugh, J. T. 1994. Relationship between thymidine metabolism, bacterioplankton community metabolic capabilities and sources of organic matter used for growth. Microbial Ecology 28: 117-131.

* Hollibaugh, J.T. 1993. Consistent patterns of thymidine metabolism by bacterioplankton communities: A clue to community composition and to the carbon sources used for growth? In: C. Pedros-Alios and R. Guerrero, [Eds]: Proceedings of the Sixth International Symposium on Microbial Ecology, Barcelona Spain, 7-11 September, 1992. pp. 471-474.

Hollibaugh, J. T., R. W. Buddemeier, and S. V. Smith. 1991. Contributions of colloidal and high molecular weight dissolved material to alkalinity and nutrient concentrations in shallow marine and estuarine systems. Marine Chemistry 33: 1-27.

Hollibaugh, J. T. et al. 1988. Tomales Bay, California: a 'macrocosm' for examining biogeochemical coupling at the land-sea interface. Eos 36: 843-845.

* Hollibaugh, J. T. and P. S. Wong. 1992. Ethanol-extractable substrate pools and the incorporation of thymidine, L-leucine and other substrates by bacterioplankton. Canadian Journal of Microbiology 38: 605-613.

* Hopkins, T. E. 1993. The physiological ecology of bat rays, Myliobatis californica, in Tomales Bay, California. PhD dissertation in Ecology, U. Ca., Davis. 104 pp.

* Joye, S. B. 1993. Spatial and temporal patterns of nitrogen fixation and denitrification in the intertidal and subtidal sediments of a Mediterranean-type estuary: Tomales Bay, California. Ph.D. thesis, UNC Chapel Hill, 227 pp.

* Joye, S.B., and J.T. Hollibaugh. 1995. Sulfide inhibition of nitrification influences nitrogen regeneration in sediments. Science 270: 623-625.

* Joye, S. B., M. L. Mazzotta, and J. T. Hollibaugh. In press. Community metabolism in microbial mats: the role of iron and manganese reduction. Applied and Environmental Microbiology.

* Joye, S. B., and H. W. Paerl. 1993. Nitrogen fixation and denitrification in the intertidal and subtidal environments of Tomales Bay, California. pp. 633-653 In: R. S. Oremland (ed.) The Biogeochemistry of Global Change: Radiatively Active Trace Gases. Chapman and Hall, NY.

* Joye, S. B., and H. W. Paerl. 1993. Contemporaneous nitrogen fixation and denitrification in marine microbial mats: rapid response to runoff events. Marine Ecology--Progress Series 94: 267-274.

* Joye, S.B. and H. W. Paerl. 1994. Nitrogen cycling in marine microbial mats: rates and patterns of denitrification nitrogen fixation. Marine Biology 119: 285-295.

* Joye, S. B., and H. W. Paerl. submitted. Nitrogen and carbon fixation rates in benthic intertidal communities in Tomales Bay, California, effects of terrestrial organic loading. Environmental Biology.

* Joye, S. B., S. V. Smith, J. T. Hollibaugh, H. W. Paerl.1996. Estimating denitrification rates in estuarine sediments: a comparison of stoichiometric and acetylene based methods. Biogeochemistry 33: 197-215.

Kimmerer, W. J. 1993. Distribution patterns of zooplankton in Tomales Bay, California. Estuaries 16: 264-272.

* Kimmerer, W. J., S. V. Smith, and J. T. Hollibaugh. 1993. A simple heuristic model of nutrient cycling in an estuary. Estuarine, Coastal and Shelf Science 37: 145-159.

* Largier, J. L., C. J. Hearn, and D. Chadwick. 1997. Density structures in low inflow estuaries. pp. 227-241 In David G. Aubrey and Carl T. Friedrichs (eds.) Buoyancy Effects on Coastal and Estuarine Dynamics. Coastal and Estuarine Studies volume 53, AGU.

* Largier, J.L., J.T. Hollibaugh, and S.V. Smith. 1997. Seasonally hypersaline estuaries in mediterranean-climate regions. Estuarine, Coastal and Shelf Science 44: 789-797.

* Murray, A.M. 1994. Community Fingerprint Analysis: A Molecular Method for Studying Marine Bacterioplankton Biodiversity. M.S. thesis, Dept. Biology, San Francisco State University. 93 pp.

* Murray, A. M., J. T. Hollibaugh, and C. Orrego. In press. Comparison of the phylogenetic compositions of bacterioplankton in two California estuaries by denaturing gradient gel electrophoresis of 16S rRNA gene fragments. Applied and Environmental Microbiology 62:

Oberdorfer, J. A., M. A. Valentino, and S. V. Smith. 1990. Groundwater contribution to the nutrient budget of Tomales Bay, California. Biogeochemistry 10: 199-216.

* Paerl, H. W. 1992. Epi- and endobiotic interactions of cyanobacteria. In: W. Reisser (ed.) Algae and Symbioses. Biopress Limited, Bristol, England. pp. 537-566.

* Paerl, H. W. 1993. Interaction of nitrogen and carbon cycles in the marine environment. pp. 343-381 In: T. Ford (ed.) Aquatic microbiology: An ecological approach. Blackwell Scientific, Oxford.

* Paerl, H. W., B. M. Bebout, S. B. Joye, D. J. DeMarias. 1993. Microscale characterization of dissolved organic matter production and uptake in marine microbial mat communities. Limnology and Oceanography 38: 1150-1161.

* Paerl, H.W., S. B. Joye, M. Fitzpatrick. 1993. Evaluation of nutrient limitation of CO₂ and N₂ fixation in marine microbial mats. Marine Ecology--Progress Series 101: 297-306.

* Peak, S. 1994. The effect of changing bathymetry on salinities and flushing times in Tomales Bay, California: 1861-1994, Honours thesis, University of New South Wales, Australian Defence Force Academy, ACT, Australia, 174 pp.

* Plant, J. N. 1995. Effects of land use change on Tomales Bay, California: new ideas from old tracers. M.S. thesis in Oceanography, U. Hawaii, 103 pp.

* Popp, B. N., F. J. Sansone, T. M. Rust, D. A. Merritt. 1995. Determination of concentration and carbon isotopic composition of dissolved methane in sediments and nearshore waters. Analytical Chemistry 34: 405-411.

* Rooney, J. J. 1995. Determination of sedimentation rates in Tomales Bay, California using a geographic information system. MS thesis, U. Hawaii, 95 pp.

* Rooney, J. J., and S. V. Smith. In press. Tomales Bay, California, sedimentation rates and watershed landuse. Journal of Coastal Research.

* Rust, T. M. 1993. The relative importance of processes controlling the distribution of methane in Tomales Bay, California. MS thesis, U. Hawaii, 76 pp.

* Sansone, F. J., J. T. Hollibaugh, S. M. Vink, R. M. Chambers, S. B. Joye, B. N. Popp. 1994. Diver-operated piston corer for nearshore use. Estuaries 17: 716-720.

* Sansone, F. J., T. M. Rust, and S. V. Smith. 1998. Methane distribution and cycling in Tomales Bay, California. Estuaries 21: 66-77.

Smith, S. V. 1991. Stoichiometry of C:N:P fluxes in shallow-water marine ecosystems. Chapter 13 in Proceedings of the Third Cary Conference: Comparative analyses of ecosystems: patterns, mechanisms and theories, p. 259-286.

* Smith, S. V. 1995. Net carbon metabolism of oceanic margins and estuaries: estimates of steady-state conditions, and speculations about anthropogenic perturbations of that steady state. p. 246-250 In: G. M. Woodwell (ed.) Biotic Feedbacks in the Global Climate System: Will the Warming Speed the Warming? Oxford U.

Smith, S. V. 1995. Reflections on the measurement and significance of carbon metabolism on coral reefs. Working paper for SCOR WG 104; on the WWW Home Page for that working group; also put out as an Open File Report of the Kansas Geological Survey.

* Smith, S. V., and M. J. Atkinson. 1994. Mass balance of nutrient fluxes in coastal lagoons. p. 133-155 In B. Kjerfve (ed.) Coastal Lagoon Processes, Elsevier.

* Smith, S. V., R. M. Chambers, and J. T. Hollibaugh. 1996. Dissolved and particulate nutrient transport through a coastal watershed-estuary system. Journal of Hydrology 176: 181-203.

Smith, S. V., and J. T. Hollibaugh. 1989. Carbon-controlled nitrogen cycling in a marine 'macrocosm': an ecosystem-scale model for managing cultural eutrophication. Marine Ecology--Progress Series 52: 103-109.

* Smith, S. V., and J. T. Hollibaugh. 1993. Coastal metabolism and the oceanic organic carbon balance. Reviews of Geophysics 31: 75-89.

* Smith, S. V., and J. T. Hollibaugh. 1997. Annual cycle and interannual variability of ecosystem metabolism in a temperate climate embayment. Ecological Monographs 67: 509-533.

*Smith, S. V., and J. T. Hollibaugh. 1998. Carbon-nitrogen-phosphorus cycling in Tomales Bay, California. Aquatic Geochemistry 4: 395-402.

* Smith, S. V., J. T. Hollibaugh, S. J. Dollar, and S. Vink. 1989. Tomales Bay, California: a case for carbon-controlled nitrogen cycling. Limnology and Oceanography 34: 37-52.

* Smith, S. V., J. T. Hollibaugh, S. J. Dollar, and S. Vink. 1991. Tomales Bay metabolism: C-N-P stoichiometry and ecosystem heterotrophy at the land-sea interface. Estuarine, Coastal and Shelf Science 33: 223-257.

Smith, S. V., and F. T. Mackenzie. 1987. The ocean as a net heterotrophic system: Implications from the carbon biogeochemical cycle. Global Biogeochemical Cycles 1: 187-198.

* Smith, S. V., and F. T. Mackenzie. 1991. Comments on the role of oceanic biota as a sink for anthropogenic CO2 emissions. Global Biogeochemical Cycles 5: 189-190.

Smith, S. V., W. J. Wiebe, J. T. Hollibaugh, S. J. Dollar, S. W. Hager, B. E. Cole, G. W. Tribble, and P. A. Wheeler. 1987. Stoichiometry of C, N. P, and Si fluxes in a temperate-climate embayment. Journal of Marine Research 45: 427-460.

* Snidvongs, A. 1993. Geochemistry of organic particulates in shallow water continental shelf environments. PhD Dissertation, U. Hawaii, 201 pp.

* Vink, S. 1994. Sedimentary phosphorus cycling in Tomales Bay, California. PhD Dissertation, U. Hawaii, 169 pp.

* Vink, S., R. M. Chambers, and S. V. Smith. 1997. Distribution of phosphorus in sediments from Tomales Bay, California. Marine Geology 39: 157-179.

Walsh, T. W. 1989. Total dissolved nitrogen in seawater: a new high-temperature combustion method and comparison with photo-oxidation. Marine Chemistry 26: 295-311.

* Walsh, T. W., S. V. Smith, and S. Vink. 1991. Review of particulate C:N:P methods used by UH/HIMB Analytical Services. pp. 91-96 In: D. C. Hurd and D. W. Spencer (eds.) Geophys. Monogr. 63, Marine Particles: Analysis and Characterization.