Caffrey, J.M., M.C. Murrell, K.R.S Amacker, J. Harper, S. Phipps, and M. Woodrey. 2014 Sustained observations of estuarine metabolism in 3 estuaries in the northeast Gulf of Mexico. Estuaries and Coasts invited Special Issue, “Drivers of Change in Shallow Coastal Photic Systems" 37: 222-241. http://dx.doi.org/10.1007/s12237-013-9701-5

Yvon-Durocher, G., J. M. Caffrey, A. Cescatti, M. Dossena, P. del Giorgio, J.M. Gasol, J.M. Montoya, J. Pumpanen, P.A. Staehr, M. Trimmer, G. Woodward & A.P. Allen. 2012. Reconciling differences in the temperature-dependence of ecosystem respiration across time scales and ecosystem types. Nature 487: 472-476.

Mortazavi, B., A.A. Riggs, J.M. Caffrey, H. Genet, and S.W. Phipps. 2012. The contribution of benthic nutrient regeneration to primary production in a shallow eutrophic estuary, Weeks Bay, Alabama. Estuaries and Coasts. 35:862-877.

Bagui, S., J. Brown, J. Caffrey, S. Bagui. 2012. Designing a relational database for tracking and analysis of atmospheric deposition of mercury and trace metals in the Pensacola Bay Watershed. International Journal of Sustainable Society. 4: 240-265.

Caffrey, J.M., W.M. Landing, S.D. Nolek, K.J. Gosnell, S.S Bagui, and S.C. Bagui. 2010 Atmospheric deposition of mercury and major ions to the Pensacola (Florida) watershed: spatial, seasonal, and inter-annual variability. Atmospheric Chemistry and Physics 10:1-24.

Landing, W.M., J.M. Caffrey, S.D. Nolek, K.J. Gosnell and W.C. Parker. 2010. Atmospheric deposition of mercury and other trace elements in Pensacola, Florida. Atmospheric Chemistry and Physics 10:4867-4877.

Caffrey, J.M., N. Bano, J.T. Hollibaugh and J. Haskins. 2010.Effects of upwelling on short-term variability in microbial and biogeochemical processes in estuarine sediments from Elkhorn Slough, California, USA. Aquatic Microbial Ecology. 58: 261-271.

Murrell, M.C., J.G. Campbell, J.D Hagy III, and J.M. Caffrey. 2009. Effects of irradiance on benthic and water column processes in a Gulf of Mexico estuary: Pensacola Bay, Florida, USA. Estuarine Coastal and Shelf Science.81:501-512.

Smith, K.A. and J.M. Caffrey. 2009. The effects of human activities and extreme meteorological events on sediment nitrogen dynamics in an urban estuary, Escambia Bay, Florida, USA. Hydrobiologia. 627:67-85.

Caffrey, J.M., N. Bano, K. Kalanetra and J. T. Hollibaugh. 2007. Ammonia-oxidation and ammonia oxidizing Bacteria and Archaea from estuaries with differing histories of hypoxia. ISME Journal 1:660-662.

Caffrey, J.M., T.P. Chapin, H.W. Jannasch, and J.C. Haskins. 2007. High nutrient pulses, tidal mixing and biological response in a small California estuary, Elkhorn Slough, CA, USA: variability in nutrient concentrations from hourly to decadal time scales. Estuarine, Coastal and Shelf Science 71: 368-380.

Caffrey, J.M., M.C. Murrell, C. Wigand and R. McKinney. 2007. Effect of nutrient loading on biogeochemical and microbial processes in a New England high salt marsh. Biogeochemistry 82:251-264.