The AquaCrop model was developed to replace the former FAO I&D Paper 33 procedures for the estimation of crop productivity in relation to water supply and agronomic management in a framework based on current plant physiological and soil water budgeting concepts. This paper presents the software of AquaCrop for which the concepts and underlying principles are described in the companion paper (Steduto et al., 2009). Input consists of weather data, crop characteristics, and soil and management characteristics that define the environment in which the crop will develop. Algorithms and calculation procedures modeling the infiltration of water, the drainage out of the root zone, the canopy and root zone development, the evaporation and transpiration rate, the biomass production, and the yield formation are presented. The mechanisms of crop response to cope with water shortage are described by only a few parameters, making the underlying processes more transparent to the user. AquaCrop is a menu-driven program with a well-developed user interface. With the help of graphs which are updated each time step (1 d) during the simulation run, the user can track changes in soil water content, and the corresponding changes in crop development, soil evaporation and transpiration rate, biomass production, and yield development. One can halt the simulation at each time step, to study the effect of changes in water related inputs, making the model particularly suitable for developing deficit irrigation strategies and scenario analysis.