Seasonal changes in spatial structure of biomass of submerged aquatic vegetation (SAV) and environmental variables were evaluated in Celestun Lagoon, an estuarine habitat in Mexico. Geostatistical techniques were used to evaluate spatial autocorrelation and to predict the spatial distribution by kriging. The relative contribution of 11 environmental variables in explaining the spatial structure of biomass of SAV was evaluated by canonical correspondence analysis. Spatial partitioning between species of SAV was evident: the seagrasses Halodule wrightii and Ruppia maritima dominated the seaward and central zones of the lagoon, respectively, whereas the green alga Chara fibrosa was constrained to the inner zone. The spatial structure and seasonal variability of SAV biomass were best explained by organic carbon in the sediments, salinity and total suspended solids in the water column. Analysis at different spatial scales allowed identifying the importance of spatial structure in biotic and abiotic variables of this estuarine habitat.