The trophic, chemical and ecological state of a lagoon is strongly influenced by numerous aspects, among which the quantity and quality of the water coming from its drainage basin are a priority. The Source-to-Sea approach directly addresses the linkages between land, water, delta, estuary, coast, nearshore and ocean ecosystems to identify appropriate courses of action to address alterations of key flows, resulting in economic, social and environmental benefits. Hydrodynamic modeling has become a fundamental tool for describing the dynamics of marine environments, and a specific field of development of ongoing research is a detailed representation of the land–coastal–sea fluxes. In the present study, a numerical modeling tool was used in the Venice Lagoon to assess and quantify dominant contributions from the river basin within specific areas of the lagoon. An advective–diffusive model was used to reproduce the transport of passive tracers. The results were analyzed using an automated computational tool, obtaining the average percentage contribution of each input from the drainage basin and mean concentrations of tracer in the different water bodies. Through the proposed methodology, it is possible to support the planning of specific measures, identifying priorities of management intervention and preliminarily exploring different scenarios.