This paper is about the morphological and biogeographical changes in São Mateus River mouth in Espírito Santo State, southeast of Brazilian coast between 1970 and 2017. During this period the mangrove ecosystem had been disrupted by fluvial-marine processes that affect this part of coast causing several problems to the county of Conceição da Barra as well as to the navigation, to the fisherman and tourism. The evolution of this part of the coast shows that fluvial-marine processes and the precipitation along the basin of São Mateus River changed drastically in 1991 by increased precipitation along the watershed and, consequently, increasing the amount of water at the mouth modifying the estuarine features, which suffered erosion and deposition on the mangroves and restinga. On the other hand, these processes also led to the colonization of new areas by mangroves. These processes are being monitored by a research project which measures the damages over the mangroves and the replacement of another types of vegetation since 1995. This paper presents the changes in morphology in a systemic perspective integrating the vegetation and pluvial attributes in the basin of São Mateus River.