Quantifying where, when, and how much denitrification occurs on the basis of measurements alone remains particularly vexing at virtually all spatial scales. As a result, models have become essential tools for integrating current understanding of the processes that control denitrification with measurements of rate-controlling properties so that the permanent losses of N within landscapes can be quantified at watershed and regional scales. In this paper, we describe commonly used approaches for modeling denitrification and N cycling processes in terrestrial and aquatic ecosystems based on selected examples from the literature. We highlight future needs for developing complementary measurements and models of denitrification. Most of the approaches described here do not explicitly simulate microbial dynamics, but make predictions by representing the environmental conditions where denitrification is expected to occur, based on conceptualizations of the N cycle and empirical data from field and laboratory investigations of the dominant process controls. Models of denitrification in terrestrial ecosystems include generally similar rate-controlling variables, but vary in their complexity of the descriptions of natural and human-related properties of the landscape, reflecting a range of scientific and management perspectives. Models of denitrification in aquatic ecosystems range in complexity from highly detailed mechanistic simulations of the N cycle to simpler source–transport models of aggregate N removal processes estimated with empirical functions, though all estimate aquatic N removal using first-order reaction rate or mass-transfer rate expressions. Both the terrestrial and aquatic modeling approaches considered here generally indicate that denitrification is an important and highly substantial component of the N cycle over large spatial scales. However, the uncertainties of model predictions are large. Future progress will be linked to advances in field measurements, spatial databases, and model structures.