Dairy farms comprise a complex landscape of groundwater pollution sources. The objective of our work is to develop a method to quantify nitrate leaching to shallow groundwater from different management units at dairy farms. Total nitrate loads are determined by the sequential calibration of a sub-regional scale and a farm-scale three-dimensional groundwater flow and transport model using observations at different spatial scales. These observations include local measurements of groundwater heads and nitrate concentrations in an extensive monitoring well network, providing data at a scale of a few meters and measurements of discharge rates and nitrate concentrations in a tile-drain network, providing data integrated across multiple farms. The various measurement scales are different from the spatial scales of the calibration parameters, which are the recharge and nitrogen leaching rates from individual management units. The calibration procedure offers a conceptual framework for using field measurements at different spatial scales to estimate recharge N concentrations at the management unit scale. It provides a map of spatially varying dairy farming impact on groundwater nitrogen. The method is applied to a dairy farm located in a relatively vulnerable hydrogeologic region in California. Potential sources within the dairy farm are divided into three categories, representing different manure management units: animal exercise yards and feeding areas (corrals), liquid manure holding ponds, and manure irrigated forage fields. Estimated average nitrogen leaching is 872 kg/ha/year, 807 kg/ha/year and 486 kg/ha/year for corrals, ponds and fields respectively. Results are applied to evaluate the accuracy of nitrogen mass balances often used by regulatory agencies to assess groundwater impacts. Calibrated leaching rates compare favorably to field and farm scale nitrogen mass balances. These data and interpretations provide a basis for developing improved management strategies.