Life cycle assessments (LCAs) play a strategic role in improving the environmental performance of a company and in supporting a successful marketing communication. The high impact of the food industry on natural resources, in terms of water consumption and greenhouse gases emission, has been focusing the attention of consumers and producers towards environmentally sustainable products. This work presents a comprehensive approach for the joint evaluation of carbon (CF) and water (WF) footprint of the wine industry from a cradle to grave perspective. The LCA analysis is carried out following the requirements of international standards (ISO/TS 14067 and ISO 14046). A complete review of the water footprint methodology is presented and guidelines for all the phases of the evaluation procedure are provided, including acquisition and validation of input data, allocation, application of analytic models, and interpretation of the results. The strength of this approach is the implementation of a side-by-side CF vs. WF assessment, based on the same system boundaries, functional unit, and input data, that allows a reliable comparison between the two indicators. In particular, a revised methodology is presented for the evaluation of the grey water component. The methodology was applied to a white and a red wine produced in the same company. A comparison between the two products is presented for each LCA phase along with literature results for similar wines.