This chapter discusses the implications of low‐input systems for nitrogen (N) and water‐use efficiency. It deals with crop yield efficiency, which refers to the relationship between yield and N application rate, and N recovery efficiency. The chapter focuses on several management strategies that are common, although not necessarily universal, to low input systems. It describes water‐use efficiency when discussing the results of the Rodale Research Center experiments. The chapter explains the absence of or minimal use of pesticides in low‐input systems. It considers the effects on soil structure and biological activity, and the implications of these effects on N losses and nitrogen‐use efficiency (NUE). In order to optimize NUE in low‐input systems, a greater understanding of the biological, chemical, and physical processes occurring in low‐input systems is needed. Soil organic matter tends to be greater in cropping systems utilizing crop rotations than in continuous cropping, and in systems utilizing animal manures rather than commercial fertilizers.