Crop rotation is a critical management strategy available to farmers to sustain soil fertility, combat pests, and improve crop yields. Because of the complex feedbacks occurring in the soil-plant-atmosphere continuum, legacy effects and their interactions with climate are generally not well understood, and their ultimate influence on yields and environmental quality is difficult to predict. Crop simulation models offer a way of parsing through this complexity. This chapter illustrates how crop models account for the interactions between soil, genotypes, management, and climate, on crops grown in various rotations, and their effects on yield and environmental outcomes (e.g. nitrate leaching, soil organic carbon sequestration) under current and future climate scenarios by presenting two different case studies and modeling approaches. The authors conclude the chapter by summarizing the advantages and disadvantages of the modeling approaches and offer some recommendations for how to best capture legacy effects.