Her research focuses on the environmental and equity dimensions of intensive food production. Working at the intersection of environment and economics, Naylor has been involved in a number of field-level research projects throughout the world concerning issues of aquaculture and livestock production, high-input agricultural development, biotechnology, climate-induced yield variability, and food security. Her research appears regularly in Science and Nature and recent articles have focused on how changing and increasingly variable climate may affect food production in developing countries.