The spatial structure of salinity, submerged aquatic vegetation (SAV) and 4 shrimp (Farfantepenaeus spp.) populations along an estuarine habitat was evaluated seasonally, based on data gathered every 1 km along a 1-dimensional transect in Celestun Lagoon, Mexico. Geostatistical techniques were used to evaluate autocorrelation among data points along the transect, and to predict their spatial distribution by kriging. The estuarine habitat was characterized by persistent salinity gradients, decreasing from the seaward (1 km) to the inner (18 km) zone of the lagoon. SAV biomass was almost always spatially structured and best described by spherical variograms. Spatial partitioning between SAV species 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. Shrimp abundance also presented a marked spatial structure best described by spherical variograms. Spatial structure of shrimps, discriminated by species (F. aztecus, F. brasiliensis, F. duorarum and F. notialis) and population components (recruits, juveniles, subadults) was most evident in the Nortes season (i.e. the season of strong northerly winds) and poorly defined in the Dry season. Spatial partitioning among species and population components was not detectable. Total shrimps and recruits were generally most abundant close to the mouth of the lagoon, although juvenile and subadult abundance peaked farther from the mouth than recruits. Distance from the mouth was the most important factor determining the spatial distribution of shrimps along the estuarine habitat. At local scales, abundance and type of SAV beds were crucial factors determining the abundance and spatial distribution of shrimps. Analysis at different spatial scales allowed us to identify the importance of spatial structure in biotic and abiotic variables of this estuarine habitat.