Understanding spatial dynamics and creating spatial boundaries of marine food webs is an important topic that resource managers are beginning to understand. Food web structure, mediated by spatial and habitat differences, was examined in a subtropical estuary using stomach content and stable isotope analyses. The goal of this study was to characterize the trophic structure in subtidal oyster reef, intertidal marsh edge, and nonvegetated bottom habitats. Fish and macroinvertebrates were sampled seasonally from July 2006 to April 2007. Spatially, the lower region of the bay supported a more robust food web, with more species and links (72 and 130, respectively) than the upper bay (63 and 87, respectively). Trophic levels (determined by ¹⁵N) and carbon sources (determined by ¹³C) were combined with dietary links (determined by stomach contents), relative population levels, and linkage strength (determined by food volume) to construct 5 dimensional food web diagrams for the 2 regions and 3 habitats studied. The ¹⁵N isotope indicated differences in trophic levels and probable nitrogen sources among regions whereas the ¹³C isotope inferred differences in carbon sources among regions in the Lavaca Bay ecosystem. This evidence suggests that lower Lavaca Bay is providing an environment conducive to robust food webs, and that locations in relatively close proximities within the same estuary can have very different food web interactions. Our data suggest there are significant differences in food web structure at the spatial scales examined in Lavaca Bay, which supports the idea that food webs are compartmentalized. As resource managers move toward ecosystem-based management, they must consider the distinct communities and accompanying food webs associated with the varying habitat types and spatial scales observed in this coastal ecosystem.