Marine protected areas are not established in an institutional and governance vacuum and managers should pay attention to the wider social-ecological system in which they are immersed. This article examines Islas Choros-Damas Marine Reserve, a small marine protected area located in a highly productive and biologically diverse coastal marine ecosystem in northern Chile, and the interactions between human, institutional, and ecological dimensions beyond those existing within its boundaries. Through documents analysis, surveys, and interviews, we described marine reserve implementation (governing system) and the social and natural ecosystem-to-be-governed. We analyzed the interactions and the connections between the marine reserve and other spatially explicit conservation and/or management measures existing in the area and influencing management outcomes and governance. A top-down approach with poor stakeholder involvement characterized the implementation process. The marine reserve is highly connected with other spatially explicit measures and with a wider social-ecological system through various ecological processes and socio-economic interactions. Current institutional interactions with positive effects on the management and governance are scarce, although several potential interactions may be developed. For the study area, any management action must recognize interferences from outside conditions and consider some of them (e.g., ecotourism management) as cross-cutting actions for the entire social-ecological system. We consider that institutional interactions and the development of social networks are opportunities to any collective effort aiming to improve governance of Islas Choros-Damas marine reserve. Communication of connections and interactions between marine protected areas and the wider social-ecological system (as described in this study) is proposed as a strategy to improve stakeholder participation in Chilean marine protected areas.