Soil acidity increasingly limits production in agricultural systems in many parts of the world. Whereas in some cases the acidity is naturally occurring, in many others agricultural practices have accelerated soil acidification. A range of management practices has been proposed to control and ameliorate soil acidification. Liming has undoubtedly received most attention, but other options that have been suggested include the application of alternative ameliorants as well as modification of the production system through changes in crops grown, fertilizer, or residue management (see Chapters 12 and 13). Laboratory tests and field trials have assessed the effectiveness of many of these practices in increasing pH and reducing aluminum activity. Results have, however, often been variable. This is probably due to interactions with other processes operating in the system as well as the influence of weather and soil variability. Simulation models can be used to address these issues by integrating and extrapolating experimental observations. In this chapter we describe how incorporation of a proton budget framework into two models of agricultural systems provides us with tools to analyze soil acidification as a function of soil, climate, and agricultural management.