In the Weser estuary, the demands Natura 2000 and the Water Framework Directive, and the need for accessibility and development of ports, along with port related activities and coastal defence all come into conflict. As there will be a constant need for dredging of the shipping channel and for security measures against sea level rise, any solution for a better conservation of the Weser estuary must be based on the integration of the different public interests and on cooperation between the authorities and the land users.

Management coordination and integration is also an issue in the Weser estuary, as there are a number of working groups dealing with the implementation of management measures relating to Natura 2000 and the Water Framework Directive, and various institutions from the Bundesländer of Bremen and Lower Saxony are involved. The aim is to get one management plan for the whole estuary, with each state in charge of measures on its territory.