This article analyzes the changes taking place in the governance of transboundary river basins located within the institutional framework of the larger de la Plata river basin. The article illustrates the changes in scale affecting the governance of water resources in the region by discussing the cases of the transboundary basins of the Apa river (Brazil-Paraguay) and the Quarai river (Brazil-Uruguay). Using these examples, I emphasise the distinction between transnational and transboundary basins: In this case, only the Quarai river basin has the double character of trans-national and trans-boundary. This case also shows that cooperation policies in water resources management form part of a broader set of cooperation initiatives related to cross-border interactions.