This paper describes calibration methods for models of agricultural production and water use in which economic variables can directly interact with hydrologic network models or other biophysical system models. We also describe and demonstrate the use of systematic calibration checks at different stages for efficient debugging of models. The central model is the California Statewide Agricultural Production Model (SWAP), a Positive Mathematical Programming (PMP) model of California irrigated agriculture. We outline the six step calibration procedure and demonstrate the model with an empirical policy analysis.