The objective of this study was to propose a multidimensional model capable of evaluating, in a participatory method, the pressures agricultural production systems cause to aquatic ecosystems. The model was structured with information compiled from scientific articles, doctoral theses, public documents, and field research performed with the participation of stakeholders through interviews, questionnaires, and group evaluations. The evaluation matrix combines seven criteria and twenty-five sub-criteria with different weights to evaluate two main aspects: (i) land occupation and soil management and (ii) agricultural waste production and disposal. The model was tested in 14 agricultural farms, representing four productive arrangements, in a large watershed (2400 km2) in southern Brazil. The geophysical characteristics of the site (18.3%), land use and occupation (28.2%), management practices (soil and water) (25.4%), manure and fertilizers (12.6%), pesticides (14.1%), agricultural waste and discards (1.4%) were the criteria and their respective weights used in the structure of the proposed evaluation model. The evaluation showed that the combination of the fragility of cultivated environments and the absence of conservation practices represented the greatest risks (72.9%) to maintaining the sound environmental conditions of aquatic ecosystems. For future research, it is recommended that a cost-effectiveness analysis be carried out to evaluate environmental conflicts.