This paper focuses on the challenges for the co-implementation of two European Union Directives, i.e., the Habitats Directive and the Water Framework Directive, for the management of Mediterranean coastal lagoons as protected areas. Many of these ecosystems are included in the Natura 2000 network, the largest network of protected areas in the world. Based on semi-structured interviews with 45 stakeholders from 41 institutions, the study identified five main types of perceived barriers: economic, political and socio-cultural, historical, administrative, and ecological. The study confirmed that the co-implementation of the Habitats Directive (HD) and the Water Framework Directive (WFD) in Mediterranean coastal lagoons generated multiple and interrelated barriers. Beyond their regulatory complexity, these EU directives confronted managers with deep operational challenges. First, mismatches between administrative and ecological boundaries weakened their ability to control key ecological processes such as nutrient flows. Second, the proliferation of indicators, often perceived as disconnected from local realities, reinforced the critique of a management by numbers approach. Finally, the widespread use of regulatory exemptions, while intended to adapt EU rules to local contexts, frequently fueled persistent mistrust among stakeholders, especially in historically degraded environments. These challenges were further exacerbated by a siloed organization of administrations, limiting coordination and adaptive management. Overall, these findings call for more integrated governance frameworks, a more critical and context-sensitive use of indicators, and greater transparency in derogation procedures.