Water pollution in the Venice Lagoon and its catchment is a main environmental issue. In Italy public funds are made available by specific national and regional regulations in order to support the realisation of initiatives for the abatement of pollutant loads that travel from the catchment into the lagoon.Local agencies in charge of water management may apply for funds by presenting suitable projects in the field of hydraulic and environmental engineering particularly modifications to the surface water network aimed at reducing diffuse pollutant loads in the Venice Lagoon. Because the need to support those agencies in choosing among options often arises, together with the need of presenting and supporting choices that are made, in front of the funding administration. The decisional context of the present study was determined by a given amount of public funds made available by the regional administration, to be used in an optimal way by choosing what to do (within a list of possible interventions like flow regulation, plantation of riparian vegetation, etc.) and where (within the surface water network of the district).A multi-stage multi-criteria evaluation approach was developed, which subdivided the decisional problem into two operational phases.In a first step a priority sub-area was chosen within the district with a multi-criteria evaluation procedure which took into account several decisional criteria, formulated by the authority responsible for the decision. Those criteria were quantified by using thematic maps (GIS layers), as spatial indicators for prioritising the location of pollution control initiatives.In a second step the choice among alternative projects within the chosen area was supported by a second round of multi-criteria analysis developed in collaboration with a decisional board.The results of the application of the proposed method to the case study demonstrated the potentials of collaborative multi-criteria analysis in supporting the activity of operational agencies during the whole process of development of proposals, plans for interventions and projects, both internally to share information and build consensus within the various component of the board, and outside, in the relationship with external bodies (funding agencies, local stakeholders, etc.), to present and support the decisions proposed.