Importance of sustainable coastal governance also in the Baltic sea region has been widely recognised and since such governance has to have integrative nature that requires horizontal cross-sectorial integration as well as involvement of all governance levels and subsequently organisation of vertical integration among the levels. Besides some succesfull local cases around Europe, mainly special outside projects based, there is to be recognized that the municipal integrated sustainable coastal governance has not been yet neither well and widely locally developed in practice nor sufficiently researched field in order to permit necessary design of adequate policy innovations. Practical development and local realisation of the municipal integrated coastal governance often encounters obstacles of the basic nature, e.g. because there are not sufficiently understood and applied cross- and trans-disciplinary approaches – studies and governance of the coastal territories as the complex social-ecological systems (SES). For understanding the process and structure of coastal governance, application of system thinking and system dynamics methods are to be emphasized as well. The paper demonstrates adaptation of coastal nature studies based System Analysis Framework (SAF) methodology for its application to coastal governance studies and general municipal governance system adjusting and upgrading towards coastal issues, what could be seen as the new step for SAF further planned developments. As the part of the EU BONUS programme BaltCoast project, the authors performed, including main stakeholders participation elements, the issue identification step, system definition and also a conceptual model building steps of the SAF methodology application in the particular, local governance innovations rich, case study territory – Salacgriva municipality in Latvia. Coastal governance problems in Latvia are especially relevant for rural coastal municipalities with limited administrative capacities and long and low populated coastline territories. The next SAF application steps will include development of coastal governance system scenarios using a systems modelling tool and the design and testing of complementary set of governance instruments as science-policy interface, that shall support sustainable use of coastal resources in the interests of coastal nature and culture protection, and local socio-economic development.