AbstractMediterranean ecosystems are in the spotlight of tourism activities, with the local populations trying to make the most of them, while in parallel, the stress signs, such as habitat and biodiversity degradation, increased pollution, or beach erosion, have begun to emerge. Furthermore, this combination of exotic and delicate qualities accompanied by excessive tourist flows leads to the imperative need for sustainable tourism development studies in these areas. In the current study, aiming to develop a new holistic framework for assessing Carrying Capacity in sensitive coastal ecosystems, a combined methodology was created and tested in Balos Lagoon, a Natura 2000 area in Western Crete. The method encompasses calculating different Carrying Capacity indicators, environmental quality measurements, visitors’ perceptions identification, and finally, a multicriteria analysis to capture the stakeholders’ and local community’s viewpoints. The combined methodologies identified vital issues, including overcrowding—Effective Carrying Capacity is exceeded by 1000 people per day during the peak season—tar residue pollution, microplastics, insufficient road infrastructure and excessive car numbers exceeding capacity. Stakeholder involvement was pivotal, prioritizing twelve proposed actions to address those issues. Notably, “frequent beach clean-ups,” targeting visual impacts, emerged as the most critical action, while parking reallocation and setting a maximum daily ferry limit were also highly ranked, promising solutions to alleviate overcrowding issues. The paper offers valuable insights for future research, emphasizing the need for continuous environmental monitoring, implementation of high-priority measures, and economic valuation of natural capital. Ultimately, this research contributes to the literature by presenting a pioneering methodology for holistic assessment and sustainable tourism development in Mediterranean sensitive coastal ecosystems.