In tropical rivers, cross-ecosystem subsidies link terrestrial, freshwater, and marine food webs, yet the biological pathways and vectors of energy transfer across habitat boundaries remain poorly resolved. We investigated the role of migratory shrimp and fishes in mediating cross-habitat connectivity along the Río Espíritu Santo, Puerto Rico, which spans mountain headwaters to estuarine and coastal environments. We combined new collections from 2024–2025 with historical data (2004–2005) to assemble a spatially extensive isotopic dataset of consumers and basal resources across the marine to freshwater gradient. We then quantified energy pathways for resident predators, and migratory shrimp and mountain mullet. We found strong spatial structuring of energy sources in predators, with increasing reliance on riverine and terrestrial production upriver. Despite this, marine-derived material contributed 30–40% of predator biomass, even in upstream freshwater sites, indicating substantial upstream reliance on estuarine production. In contrast, migratory shrimp showed consistently mixed diets across the river continuum, deriving 40–60% of their biomass from marine sources and 20–40% from terrestrial sources at all sites, suggesting bidirectional energy transfer during downstream settlement and upstream migration. Mountain mullet exhibited high reliance on marine sources throughout the river, reinforcing their role as persistent upstream vectors of estuarine energy. Together, these results demonstrate that amphidromous consumers facilitate the flow of marine and terrestrial subsidies across tropical river networks and highlight the importance of biological conveyors of energy across habitat boundaries in tropical river ecosystems.