Kaushal, S.S., W.M. Lewis, Jr., and J.F. McCutchan, Jr. 2006. Land Use Change and Nitrogen Enrichment of a Rocky Mountain Watershed. Ecological Applications 16(1): 299-312 .
Lewis, W.M. Jr. et al. 2004. NRC. Endangered and Threatened Fishes in the Klamath River Basin : Causes of Decline and Strategies for Recovery. National Academies Press, Washington , D.C.
Ortiz-Zayas, J.R., W.M. Lewis, Jr., J.F. Saunders, III, J. H. McCutchan, Jr. and F. N. Scatena. 2005. Metabolism of a tropical rainforest stream. Journal of the North American Benthological Society 24(4): 769-783.
Kaushal, S.S. and W.M. Lewis, Jr. 2005. Fate and transport of organic nitrogenin minimally disturbed montane streams of Colorado , USA . Biogeochemistry 74:303-321.
McCutchan, J.H. Jr., J.F. Saunders, III, A. L. Pribyl, and W.M. Lewis, Jr. 2003. Open-channel estimation of denitrification. Limnology and Oceanography Methods 1: 74-81.
Lewis, W. M. Jr. 2002. Causes for the high frequency of nitrogen limitation in tropical lakes. Verh. Internat. Verein. Limnol. 28: 210-213.
McCutchan, J.H. Jr. and W.M. Lewis, Jr. 2002. Relative importance of carbon sources for macroinvertebrates in a Rocky Mountain stream. Limnology and Oceanography 47: 742-752.
Lewis, W. M. Jr. 2001. Wetlands Explained. Wetland Science, Policy, and Politics in America . Oxford University Press, New York , NY .