In the seascape, species migrate between ecosystems to complete their life cycles, and such ontogenetic migrations create functional connections between ecosystems. Nevertheless, the scarcity of information on patch distribution, species life history and ecology limits its application in Marine Protected Areas (MPA) management. We use a potential connectivity network approach to analyze how Haemulon flavolineatum might move through a complex and diverse seascape by simulating part of its life cycle migrations among three ecosystems (reef, mangrove, and seagrass) in the MPA of Bahía Portete-Kaurrele (BPK), Colombia. We used available ecosystem cover maps to conduct habitat fragmentation analyses and evaluate structural connectivity in BPK using eight indices that describe ecosystem patches and how they are related. With published information on the H. flavolineatum home range and its ontogenetic migration distances, we estimated the potential functional connectivity (CONNECT and migration distances) between ecosystems by building bipartite graphs. The benthic habitat configuration of the BPK could allow Haemulon flavolineatum to complete at least two stages of its life cycle (stage 5 mangroves to reefs being more likely than stage 4 seagrass to mangroves). Ontogenetic migrations is possible since, patches of different ecosystems were highly intermixed (76%) rather than grouped (58%); reefs showed higher values of structural indices (patch area, largest patch, shape complexity, functional links) than mangrove (shortest distance to the nearest neighbor) and seagrass (representativeness); and juveniles migrate from mangroves to reef patches along the bay, but they could be isolated by distance when moving from particular seagrass to mangrove patches. Our methodological approach, which integrates ecological information (evidence-based ranges of species migration distances between habitat patches) and the seascape (spatial configuration of habitat patches and fragmentation) is novel for a marine fish species with ontogenetic migration to search for the likelihood of completing its life cycle stages. We discuss the need for ecological information on French grunts and the need to validate future models and scenarios.