Waters' research centers on the epistemology of biological sciences. He has written on reductionism, pluralism, experimentation, conceptual and investigative practices, and causal reasoning. He is a prominent figure in the Philosophy of Biology literature. His most prominent and influential philosophical research is focused on a historically informed epistemological account of how scientists succeed, and why this is philosophically important.
"Shifting Attention From Theory to Practice in Philosophy of Biology" in M.C. Galavotti, D. Dieks, W.J. Gonzalez, S. Hartmann, T. Uebel, and M. Weber (eds.) New Directions in the Philosophy of Science, ed. by. Berlin: Springer International Publishing, 2014, pp. 121–139.[8]
"Beyond Theoretical Reduction and Layer-cake Antireduction: How DNA Retooled Genetics and Transformed Biological Practice", in Michael Ruse (ed.) Oxford Handbook to the Philosophy of Biology. New York, NY: Oxford University Press, 2008, pp. 238–62.[9]
"Causes that Make a Difference", The Journal of Philosophy. Volume CIV, Number 11 (2007): 551–579.[10]
"The Pluralist Stance" with Stephen Kellert and Helen Longino, in Scientific Pluralism, Volume XIX of the Minnesota Studies in the Philosophy of Science, edited with Stephen Kellert, Helen Longino, Minneapolis, MN: University of Minnesota Press, 2006, pp. 7–29
"Why Genic and Multilevel Selection Theories are Here to Stay", Philosophy of Science 72 (2) (2005): 311–33.
"The Arguments in Darwin's Origin of Species", in The Cambridge Companion to Darwin, edited by Jonathan Hodge and Gregory Radick, Cambridge: Cambridge University Press, 2003, pp. 116–139.
