Duffy, C.J., 2004, Semi-discrete dynamical model for mountain-front recharge and water balance estimation, Rio Grande of southern Colorado and New Mexico, in Groundwater Recharge in a Desert Environment: The Southwestern United States, edited by J.F. Hogan, F.M. Phillips, and B.R. Scanlon, Water Science and Applications Series, vol. 9, American Geophysical Union, Washington, D.C., 255-271.
Duffy, C and D. Brandes, 2001, Dimension Reduction and Source Identification for Multispecies Groundwater Contamination. Journal Of Contaminant Hydrology, 48 . 151-165. (Principal Author)
Newman, B.D., C.J. Duffy, and D.D. Hickmott, 2001. Evaluating the hydrogeochemical response of springs using singular spectrum analysis and phase-plane plots, in New Approaches to Characterising Groundwater Flow, edited by Seiler and Wohnlich, International Assn. of Hydrogeologists, 762-767.
K.K. Droegemeier, J.D. Smith, S. Businger, C. Doswell III, J. Doyle, C. Duffy, E. Foufoula-Georgiou, T. Graziano, L.D. James, V. Krajewski, M. LeMone, D. Lettenmaier, C. Mass, R. Pielke Sr., P. Ray, S. Rutledge, J. Schaake, and E. Zipser, Hydrological Aspects of Weather Prediction and Flood Warnings: Report of the Ninth Prospectus Development Team of the U.S. Weather Research Program. Bulletin of the American Meteorological Society, March 2000. (Contributing author)
Entekhabi, E., G. R. Asrar, A.K. Betts, K.J. Beven, R.L. Bras, C.J. Duffy, T. Dunne, R.D. Koster, D.P. Lettenmaier, D.B. McLaughlin, W. J. Shuttleworth, M.T. van Genuchten, M. Wei, E.F. Wood, 1999, An Agenda for Land-Surface Hydrology Research and a Call for the Second International Hydrological Decade, Bulletin of the American Meteorological Society, 80(10). Pp. 2043-2058.
Duffy, C. J., K. Cooley, N. Mock, D.H. Lee, 1991, Self-affine scaling and subsurface response to snowmelt in steep terrain, Journal of Hydrology, 123, 395-414.
Duffy, C. J. and D. H. Lee, 1992, Baseflow response from nonpoint source contamination: simulated spatial uncertainty in source, structure , and initial condition, Water Resources Research, 28 (3), 905-914.
Fan, Y. and C. J. Duffy, 1993, Statistical Analysis of Monthly Temperature and Precipitation Fields on the Wasatch Front, Water Resources Research, 29(12). 4157-4166.
Azimi, A., C.J. Duffy, 1993, Modeling transport of subsurface salinity from a Mancos shale hillslope, Ground Water, 31(6), 972-981.
Jin, M. and C. J. Duffy, 1994, Spectral and Bispectral Analysis for Single and Multiple Input Nonlinear Phreatic Aquifer Systems, Water Resources Research, 30(7), 2073-2095.
Duffy, C.J. 1996., A two-state internal balance model for soil moisture and groundwater dynamics in complex terrain, Water Resources Research, 32(8), 2421-2434.