1. Large-bodied, top-predators are often highly mobile, with the potential to provide important linkages between spatially distinct food webs. What biological factors contribute to variation in cross-ecosystem movements, however, have rarely been examined. 2. Here, we investigated how ontogeny (body size), sex, and individual-level behavior impacts intra-population variation in cross-ecosystem foraging (i.e., between freshwater and marine systems), by the top-predator Alligator mississippiensis. 3. Field surveys revealed A. mississippiensis uses marine ecosystems regularly and are abundant in estuarine tidal creeks (from 0.3–6.3 individuals/km of creek, n = 45 surveys). Alligator mississippiensis captured in marine/estuarine habitats were significantly larger than individuals captured in freshwater and intermediate habitats. 4. Stomach content analysis showed that small juveniles consumed marine/estuarine prey less frequently (6.7% of individuals) than did large juveniles (57.8%), sub-adult (73%), and adult (78%) size classes. Isotopic mixing model analysis (SIAR) also suggests substantial variation in use of marine/estuarine prey resources with differences among and within size classes between sexes and individuals (range of median estimates for marine/estuarine diet contribution = 0.05–0.76). 5. These results demonstrate the importance of intra-population characteristics (body size, sex, and individual specialization) as key determinants of the strength of predator-driven ecosystem connectivity resulting from cross-ecosystem foraging behaviors. Understanding the factors which contribute to variation in cross-ecosystem foraging behaviors will improve our predictive understanding of the effects of top-predators on community structure and ecosystem function.