Understanding the sources of primary production supporting marine food webs is important for conserving critical habitats. However, the importance of allochthonous versus autochthonous production is often unclear. We identify the sources of primary production supporting three species of predatory fish (Lutjanus carponotatus, Lutjanus fulviflamma, and Lethrinus punctulatus) in the Dampier Archipelago, Western Australia. The proportions of mangrove, seagrass, macroalgae, and suspended particulate organic matter (SPOM) assimilated by fish of different life-history stages and from different habitats were determined using stable isotopes and Bayesian mixing models. While contributions of sources varied among species and habitats, we found that SPOM was an important energetic resource for both adults and juveniles of all three fish species. Juvenile L. carponotatus and L. punctulatus inhabiting macroalgal habitats assimilated more seagrass- and macroalgae-derived material than fish from coral or mangrove habitats, while reliance on mangrove carbon was generally limited overall. Assimilation of macrophyte-derived material decreased throughout ontogeny for L. carponotatus, while L. fulviflamma relied on a combination of SPOM and seagrass into adulthood. The contribution of macroalgae and SPOM to the diets of juvenile L. punctulatus and L. carponotatus from macroalgal habitats varied spatially but was unrelated to seascape configuration, habitat quality, or hydrodynamic conditions. While mixing models suggested a modest degree of trophic connectivity, cross-habitat trophic subsidies provided by macrophytes play a minor role in supporting the studied fish of either life-history stage. Instead, microalgal production predominantly fuels the productivity of predatory fish in this turbid, macrotidal system.