This study explores how local communities reflect on institutional frameworks and protected area governance in two national parks (NPs) with similar nature values in Estonia and Russia, and aims to understand the role of value systems in these interactions. It is based on 50 in-depth interviews with a broad range of stakeholders, and a desktop analysis of relevant regulation and plans. Interview questions reflect on various aspects of well-being (including fairness of governance solutions), awareness of NPs’ function and restrictions, related value aspects, and covered basic personal data needed to interpret the interviews. The study reconfirms the pivotal role of social justice as a driver of wellbeing. In particular, it articulates the significance of value systems playing the role of filters between governance inputs and specific management activities of communities. It underlines the vulnerability of such systems at a community level, most of all to the impacts related to various instances of “centralization”. They are manifested through the choice of restrictive measures and top-down arrangements at the expense of transparency and inclusiveness (in Russia), as well as through the removal of governance autonomy from NPs and transferring monitoring and enforcement functions to local communities without clear mandates or sufficient capacity (in Estonia).