Estuaries in the northern Gulf of Mexico (GOM) provide habitat for many ecologically, commercially, and recreationally important fish and crustacean species (i.e., nekton), but patterns of nekton abundance and community assemblages across habitat types, salinity zones, and seasons have not been described region-wide. Recognizing the wealth of information collected from previous and ongoing field sampling efforts, we developed a meta-analytical approach to aggregate nekton density data from separate studies (using different gear types) that can be used to answer key research questions. We then applied this meta-analytical approach to separate nekton datasets from studies conducted in the Gulf of Mexico to summarize patterns in nekton density across and within several estuarine habitat types, including marsh, oyster reefs, submerged aquatic vegetation (SAV), and open-water non-vegetated bottom (NVB). The results of the meta-analysis highlighted several important patterns of nekton use associated with these habitat types. Nekton densities were higher in structured estuarine habitats (i.e., marsh, oyster reefs, SAV) than in open-water NVB habitat. Marsh and SAV community assemblages were relatively similar to each other, but different from those associated with open-water NVB and oyster habitats. Densities of commercially and recreationally important crustacean and fish species were highest in saline marshes, thus demonstrating the importance of this habitat in the northern GOM. The results of our meta-analysis are generally consistent with previous site-specific studies in the region (many of which were included in the meta-analysis) and provide further evidence for these patterns at a regional scale. This meta-analytical approach is easy to implement for diverse research and management purposes, and provides the opportunity to advance understanding of the value and role of coastal habitats to nekton communities.