In the last century sea level rose 12-22 cm on a global average and the Intergovernmental Panel on Climate Change reiterates sea level will continue to rise. Major concerns regard the intrusion of seawater into coastal low-lying ecosystems; most host a large/unique biodiversity and are vital for nature conservation (targeted by EU environmental-related Strategies/Directives, e.g. Biodiversity strategy/Habitats Directive, and other national/international legislations). Furthermore, most inhabiting freshwater and terrestrial biota is sensitive to increased salinity, being threatened in future salinized habitats. To protect biodiversity and establish safety salinity concentrations, SALTFREE project (PTDC/AAC-CLI/111706/2009) generated data for freshwater and terrestrial biota responses to increased salinity due to salt intrusion. Integrative (freshwater and soil) species sensitive distribution (SSD) curves were constructed and predictable no effects concentrations (PNECs) computed, as the resilience of freshwater and terrestrial coastal ecosystems is often interdependent. Following this, one main goal of SALTFREE II is to validate the derived PNECs under realistic scenarios of freshwater/terrestrial ecosystems, for reference/anthropogenic impacted situations (as chemical interactions may change toxicity), by conducting terrestrial model ecosystems and outdoor aquatic mesocosms at each case study. Aside from the need to protect biodiversity, most threatened coastal regions comprise large populations holding significant socio-economic activities supported by the provided ecosystem services (ES) that must also be protected. To promote their integrative protection, the iteration between the different actors (scientific community, end-users, stakeholders and local community) is fundamental to account for the main drivers and pressures combined with the supply and demand for ES. Thus, SALTFREE II knowledge base on the status of the case studies (selected along the Portuguese coast to consider regional differences in e.g. ecology/climate/socio-economic/land use; centre-Baixo Vouga Lagunar and south-Lagoa da Sancha) will be achieved by combining the scientific knowledge with the stakeholders perception obtained through participatory processes. Knowledge will be organized following a DPSIR approach, underpinning the Ecosystem Approach, by integrating human well-being and ecosystem sustainability aspects (society/economy/ecology). PNECs derived in SALTFREE will be adjusted according to this iteration and tested, in mesocosms, in reference and anthropogenically impacted situations. The scenario most protective of biodiversity will be combined with the identified ES. Results will be discussed with stakeholders to select possible trade-offs and co-develop management options. Meeting the knowledge needs of SALTFREE II research will combine natural and social sciences involving a multidisciplinary team with background in transdisciplinary approaches.