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The biogeographic regions Amazonia and the Pantanal, two areas of high biodiversity importance, have a link to each other through an ecotone formed by the upstream part of the rivers Paraguay and Guapore. The two river basins share part of their flora and fauna species and in this ecotone species exchange processes takes place. Therefore it should be considered as an important area to realize the targets for 2020 of the Convention of Biological Diversity (CBD) at the regional level. However, since over 20 years this area is under severe pressure of land conversion and is increasingly threatened by river change, due to building of hydroelectric power stations. This causes direct and indirect damaging effects on the region and on its role as biodiversity corridor. In the framework of the BioNorte project we carried out a Driver, Pressure, State, Impact, Response (DPSIR) analysis of the region and included a stakeholder analysis. The direct pressures are changes in the use of land and rivers that constitute the river ecotone between the Amazon and Pantanal. Indirect pressures are road access, opening the land for further deforestation and agricultural developments. Fragmentation of the remnant forest patches in combination with river fragmentation can cause decline in biodiversity, prevent species exchange between the Amazonia and the Pantanal and fish to spawn upstream. If river flows are being blocked, the flood pulse and the migration corridor of fish and the transport of plant seeds will be hampered. The societal response to this can be denial, a positive reaction by enforcement of traditional conservation actions or, as agreed at the COP 2010 by the Convention of Parties to the CBD as a goal for the year 2020, the integration of biodiversity targets into land development toward sustainable land use by diminishing river and forest fragmentation.