Interlinked mangrove–seagrass ecosystems are characteristic features of many tropical coastal areas, where they act as feeding and nursery grounds for a variety of fishes and invertebrates. The autotrophic carbon sources supporting fisheries in Gazi bay (Kenya) were studied in three sites, two located in the tidal creeks flowing through extensive mangrove forests, another site located in the subtidal seagrass meadows, approximately 2.5 km away from the forest. Carbon and nitrogen stable isotope composition of 42 fish species, 2 crustacean species and a range of potential primary food sources (e.g., mangroves, seagrasses and epiphytes, macroalgae) were analysed. There was considerable overlap in the δ13C signatures between fish (−16.1 ± 2.1‰), seagrasses (−15.1 ± 3.0‰), seagrass epiphytes (−13.6 ± 3.3‰), and macroalgae (−20.4 ± 3.1‰). Nevertheless, the signatures for most primary producers were sufficiently distinct to indicate that the dominant carbon sources for fish were mainly derived from the seagrass and their associated epiphytic community, and possibly macroalgae. Mangrove-derived organic matter contributes only marginally to the overall fish food web. Carbon supporting these fish communities was derived directly through grazing by herbivorous and some omnivorous fishes, or indirectly through the benthic food web. Fishes from the mangrove creeks had distinctly lower δ13C signatures (−16.8 ± 2.0‰) compared to those collected in the adjacent seagrass beds (−14.7 ± 1.7‰). This indicated that these habitats were used as distinct sheltering and feeding zones for the fishes collected, with minimal degree of exchange within the fish communities despite their regular movement pattern.