Although marine sponges are one of the most ecologically important benthic groups in marine ecosystems, their ecological role in seagrass beds from estuarine environments is little known. In this study we investigated the temporal and small-scale spatial variability in the abundance and biomass of the three common seagrass-dwelling sponges Halichondria melanadocia, Haliclona implexiformis and Chondrilla caribensis in a tropical estuary of the Southern Gulf of Mexico. The influence of biotic (physical characteristics of the seagrass) and abiotic (temperature, salinity, water movement, sediment particle size and sedimentation rate) variables on the spatio-temporal variability of these population descriptors was evaluated. In addition, a complete identification of the sponge species through morphology and COI mtDNA sequences (integrative taxonomy) was performed. Chondrilla caribensis and H. melanadocia had the highest overall average abundance and biomass, respectively. There was no significant correlation with temperature and salinity. In H. melanadocia, temporal variations in its average biomass were positively related to changes in the average size of individuals, whereas in H. implexiformis and C. caribensis these intra-annual variations in biomass were positively related to changes in their average abundance. Important declines in the average biomass and size of H. melanadocia and in the average abundance of H. implexiformis occurred during the transition period from the dry to the rainy season, which was attributed to fragmentation and shrinkage processes. Moreover, the abundance and biomass of the three sponge species showed high small-scale spatial variations within the seagrass meadow, but without a clear pattern of variation related with the distance from the shore. In H. implexiformis a significant negative relationship was found between its average biomass and the seagrass biomass. In H. melanadocia and H. implexiformis as well, their abundance was positively related with the proportion of coarse particles of the sediment (mollusk shell debris). Multivariate analyses confirmed that the proportion of coarse particles in the sediment, either acting alone or in conjunction with other variables such as seagrass shoot density and sedimentation/resuspension rate, was the variable that best explained the distribution of sponges within the seagrass meadow. This is one of the few studies on the population dynamics of sponges in seagrass meadows from estuarine environments.