According to the European Commission (2012), stakeholder participation will be crucial to the success of Blue and Green Infrastructure Networks (BGIN). BGIN development calls for originality in its process and particularly for distinctive participatory assessments of nature based solution on a territory. Planning such networks must take into account the social and economical implications and possible barriers and necessary trade-offs. The process has to embrace transdisciplinarity, be imbedded in local policies and engage stakeholders at each step. The multi-model platform developed in ALICE has been embedded in a stakeholder engagement framework that ensured pro-active interactions between scientists and stakeholders at each step of the project. Innovative landscape management has to find the right alchemy to sustain engagement while avoiding stakeholder fatigue, stay in adequacy with stakeholders needs, identify science knowledge gaps and better angle research focus, and create a dynamic discussion forum. Based on the lessons learned from the four ALICE case studies and from former participatory assessment experiments during Interreg and H2020 European projects, we developed a methodological handbook where we explore how research has not only to span several disciplines from environmental to social sciences but interact strongly with stakeholders and empower the discipline of transdisciplinarity with creative methodologies and tools. The handbook: “Towards collaborative environmental management: Road map to a participatory assessment” will be available at the end of the ALICE project as well as a web site with tools and resources: participatory-assessment.eu.