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Understanding the processes and mechanisms that determine coastal connectivity may help us to propose and establish more effective strategies for maintaining the environmental goods and services from coastal ecosystems. The eastern Yucatán Peninsula, from inland to sea range from: karstic freshwater lakes, brackish lagoons, estuarine coastal lagoons to reef lagoons. These ecosystems coalesced to form the largest and complex coastal ecosystems of the Yucatán Peninsula. The spatio-temporal structure of this complex ecosystem can be used as a model system to study connectivity processes through its hydrological, biogeochemical and ecological interactions. Based on its structure we propose a conceptual model, which we call the "Transverse Coastal Corridor" as a meaningful strategy for research, coastal development and conservation in the southeastern Yucatán Peninsula. The corridor includes the second largest freshwater karstic lake in Mexico, Laguna Bacalar; the largest estuarine-coastal lagoon, Chetumal Bay, the largest extant freshwater microbialite ecosystem and the structurally most complex coral reef ecosystem of the Mesoamerican Barrier Reef System. Physical, chemical and biological exchanges and interactions across the corridor of terrestrial, freshwater, marine environments drive a diverse and complex set of ecological processes that determine biodiversity and ecosystem functioning. We consider that the conceptual model of The Transverse Coastal Corridor may be more appealing to the different actors involved in the regional scale as it recognizes the particular biological and ecological characteristics of the interrelated ecosystems by seeking a balance from protection, management efforts, and sustainable use of the natural resources whilst preserving ecosystem functioning. Inglés