The Biodivalue project target geographical area is the Strait of Sicily south east basin, between the south east Sicilian coast, the Pelagie Islands archipelago and the islands of Malta, Gozo and Comino. This area constitutes an intensive international maritime traffic of tankers ships, cargo, passenger and Ro-Ro, fishing boats together with pleasure craft and sailing boats. The different environmental impacts especially on air, water, marine and coastal ecosystems cause negative consequences affecting the whole community. With the Biodivalue project, a system was developed for measuring the biophysical risk of biodiversity loss in the Sicilian Channel with an evaluation system for the economic consequences on the coastal communities. In particular, the project has carried out the study and analysis of maritime traffic in the Strait of Sicily, the polluting emissions produced by it and the biophysical consequences of these emissions on flora, fauna and the atmosphere in general. At the same time Biodivalue conducted an economic valuation of negative externalities caused to the marine and coastal ecosystems operational pollution from marine traffic. The data collected from studies and analysis have been put into a software called “BioDiWare” as a support tool to the administrative management of maritime traffic for choices of decision-makers helping to make the principle enshrined in international conventions, the EU and national rules effective, but in the end seldomly applied: “The polluter pays!”.