The phytosanitary diffuse pollution is a major focus for the interface of the agriculture and the environment. Its consequences for the human health and the environment urged the society to question the scientists on adequate tools of decision-making support and evaluation. In this perspective, we adopted an interdisciplinary approach between geography and agronomy in order to implement tools for a joint management of the diffuse phytosanitary pollution at the level of a territory: Merja Zerga in Morocco. Within the framework of a participatory approach, this work was based on the joint and interactive use of several interdisciplinary tools: the Geographical Information systems (GIS), the indicator of frequency of treatments (IFT), an indicator of risk of toxicity for the health of the applicator (IRSA) and for the environment (IRTE), a technical-economic platform and a simulation game. These tools enabled us to analyze the data gathered from the bibliographic research, the field statements and the surveys with the farmers and stakeholders of the territory.The results of this multi-scale analysis, from the farmer plots to the watershed basin allowed us to highlight the construction of the Merja Zerga space as a territory and to understand the consequences of the phytosanitary and agricultural practices on the human health of the applicator and on the environment, the spatial and social injustice in terms of propensity to pollute. This study based on generic tools, and going beyond the mere evaluation, constitutes an original approach for the establishment of strategies for the management of pesticides without damaging the economic sustainability of farms.