<p>Subtropical estuaries frequently support abundant and diverse faunal assemblages, but it is often unclear how these productive ecosystems are responding to climate change. In the eastern Gulf of Mexico, estuarine faunal assemblages have been sampled for decades as part of a long-term, fisheries-independent monitoring program. We assessed trends in water temperature, submerged aquatic vegetation, and the abundance, richness, and compositional structure of faunal assemblages over more than two decades in four estuarine systems using this dataset. We used both univariate and multivariate analyses to quantify and describe the dynamics of these habitat and faunal variables. Further, we separated our analyses for summer and winter seasons since the latter has been observed to experience stronger responses to climate change in other systems. Water temperature increased in all systems during summer and winter, although the rate of increase in winter was three times greater than in summer. Submerged aquatic vegetation was generally stable over time, but we observed both decreasing and increasing cover in different systems. Overall, faunal abundance and richness was generally stable over time; however, most systems exhibited slow, but significant, changes in assemblage structure, consistent with ecological drift. Further, some faunal changes were indicative of tropicalization, where nearly 30% of the species that increased in abundance had distributions centered at lower latitudes. Moreover, there was a reduction in abundance of a temperate-centered taxon across all study systems in the winter. These results reflected a combination of both stability and change in habitat and the supported faunal assemblages over the past two decades. These ecosystems should continue to be monitored as climate change has the potential to induce profound ecological shifts.</p>