This study is an application of the scientific mediation process through modeling the physical, chemical and biological impacts of a waterway construction in Mirim Lagoon. Qualitative modelling process, based on Qualitative Reasoning, was conduced to better understand the ecological impact on water environment. The qualitative reasoning simulation show clear trends towards a loss of the physiochemical natural characteristics of the lagoon (“backwater effect”) and a decline of macrofit, invertebrate, water birds and fish species. Furthermore, the simulation showed the spreading of the golden mussel (Limnoperma fortunei), which is an invasive species.