Technical Abstract: Process-based system models can greatly enhance and extend field research. However, a model of the complex agricultural system requires a number of parameters for soil, crop, and weather variables. Most often, several of these parameters are difficult to measure and have to be estimated from some related available data or calibrated to match some measured outcomes. There can be a great deal of caution required in estimating and calibrating the parameters, as well as in validation and use of the model to extend research. At present, there are no standard calibration procedures available for agriculture system models. In order to facilitate the use of models by field researchers, there is a need to develop such procedures and methodologies. Toward this goal, we present a step by step procedure for parameterization, calibration, validation, and further application of the ARS Root Zone Water Quality Model (RZWQM2) with examples for some typical experimental conditions. Theoretic description of the model is given where appropriate for the users. The procedures and methodology given here should be applicable to other similar models.