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Producing the food required by a growing population while curbing the negative environmental impacts of nitrogen (N) overfertilization is a challenge to modern agriculture. Processes occurring in soils in agricultural systems are complex since they are affected by many variables, including the type of soil, climate, crop, and management practices. These factors often result in variable conditions between sites, furthering the complexity to devise best-management practices concerning crop yield, and soil sustainability. This chapter provides an overview of the transformations occurring in agricultural soils with a special focus on nitrification and the practices that minimize nitrogen losses. A sensible plan to reduce N losses from an agricultural field requires reliable information about the N fluxes. Measurement of these N fluxes is rapidly advancing with new technologies, from field devices to satellite imaging and precision farming using UAVs. A case study of northern Mexico is briefly discussed as an example of the unique challenges faced by some of the world’s agricultural regions.