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Mangrove and mudflat food webs are segregated across four trophic levels, yet connected by highly mobile top predatorsSeascape connectivity is crucial for healthy, resilient ecosystems and fisheries. Yet, our understanding of connectivity in turbid mangrove-lined estuaries—some of the world’s most productive ecosystems—is limited to macrotidal systems, and rarely incorporates highly mobile top predators. We analysed δ13C and δ15N isotope values of 7 primary producers, 24 invertebrate taxa, 13 fishes, 4 birds and 1 reptile to reveal trophic interactions within and between a mangrove and adjacent mudflat in a microtidal system of the Gulf of Paria, Orinoco River estuary. Primary producers, invertebrates and fishes collected within the mangrove were significantly depleted in 13C and 15N compared to those collected on the mudflat. Stable isotope mixing models showed that mangrove-derived carbon was predominantly assimilated by invertebrates (78 ± 5% SE) and fishes (88 ± 11%) sampled in the mangrove. In contrast, invertebrates and fishes sampled in the mudflat derived <21% of their carbon from mangrove sources. Instead, microphytobenthos and phytoplankton underpinned the mudflat food web. Scarlet ibis Eudocimus ruber and yellow-crowned night heron Nyctanassa violacea were also highly associated with mangrove carbon sources. However, osprey Pandion haliaetus, snowy egret Egretta thula and spectacled caiman Caiman crocodilus obtained carbon from both mangrove and mudflat sources, effectively integrating the food webs. The present study demonstrates simultaneous aspects of food web segregation and connectivity, as well as the importance of surveying the entire food web across a range of tidal systems when investigating seascape connectivity.