In the Mediterranean area, there is a dense transport network that provides access to urban and tourist areas. This area is also a strategic transport corridor. It includes major infrastructures such as highways and high speed railways that will be expanded in the near future. These infrastructures put a lot of pressure on the rich biodiversity of the Mediterranean coastal wetlands that are included in the Natura 2000 Network, most of which are designated Special Protection Areas (SPAs). A research project included in the Spanish National Plan for Scientific Research, Development and Technological Innovation 2008-2011, which is supported by the Ministry of the Environment and Rural and Marine Affairs, aims to define a scheme to mitigate and prevent the impact of transport networks on wetland habitats, which are of high conservation interest. Monitoring took place during 2008 and 2009 at the Natural Park Aiguamolls de l’Empordà (Girona) and Albufera de Valencia. It included analyses of road mortality, the use of wildlife passages, the behaviour of birds crossing the infrastructures and the abundance of mammals and birds at different distances from the roads. These data have been combined with landscape analysis using GIS, which provides information about habitat distribution and connectivity features. Based on these empirical data, a scheme will be defined to identify and prioritise the most conflictive points, at which defragmentation measures or other actions will be implemented to reduce the impact on biodiversity. In addition, guidelines will be established to mitigate the existing impact and to avoid the effects of new infrastructure.