The EU Water Framework Directive (WFD) adopted an integrated approach for the management and governance of European rivers, which led Spain and Portugal to carry out coordinated hydrological planning of the international basins, considering them as unique realities from ecological, hydrological and hydrogeological perspectives. In spite of this ecosystemic basis, the Directive allowed river basin management plans (RBMPs) to cover those parts of the international river basin districts located within the territory of each member state if joint planning was not possible. Moreover, under the requirements of the Strategic Environmental Assessment Directive (SEA Directive), both countries are obliged to submit the RBMPs for SEA and to consult the authorities and the public in other states if a plan could affect the environment in a neighbouring state. In the case of the hydrological planning of the Miño river basin and its coastal and estuarine waters, the SEA was conducted through a split SEA at the level of national sub-basins. The present study analyses the findings of the two SEA procedures on the Miño river during the recent hydrological cycle under the requirements of WFD and SEA Directive. Thus, from an integrated approach adopted by WFD that demands interdependence and interrelationship between both assessments, the reality of two separated assessments revealed disconnections concerning the methodologies used, asymmetries in the detection of cross-border effects and an uneven national and transboundary participation. Overcoming these deficiencies and improving efficiency is a challenge for the new hydrological cycle. An elaboration of joint SEA between co-riparian states that could help respond to the European Union (EU) expectations from an integrated approach is recommended.