Diffuse pollution is among the major environmental concerns in terms of prevention of further deterioration and restoration of water to a "good status" in terms of ecological and chemical parameters. A step forward should be made for finding better land use, crop irrigation and fertilization practices to avoid damaging water bodies. This paper presents a framework for obtaining the decisions to be implemented in order to define a sustainable agriculture land use and production practices. A multidisciplinary approach is proposed for building a decision model capable of representing all the issues involved in the scope of an integrated management of land and water resources. The framework proposed is the basis of a research project recently financed by the Portuguese research foundation (Fundação para a Ciência e a Tecnologia). The main objectives of the project can be summarized as follows: 1) Improve the scientific knowledge regarding the interrelation between the agriculture land use and the production practices and the groundwater and the surface water quality protection, towards a more sustainable agriculture; 2) Contribute to support future decisions in terms of more adequate policies regarding rural land use planning (type of crops and associated fertilizers and treatment techniques), taking into consideration the protection of the environment based on vulnerability and risk concepts.