Modeling the distribution patterns of the estuarine macrobenthic community has revealed itself as a difficult task due to spatio-temporal heterogeneity. This study uses ordinary kriging and Poisson modeling to generate distribution maps of the subtidal benthic macrofauna in the Trapandé Bay (southeastern Brazil). Samples were taken in duplicate from 36 locations distributed along nine transects perpendicular to the main estuarine axis in October 2006 and March 2007. One-hundred and seventy taxa belonging to 12 phyla, were identified, with dominance of Annelida Polychaeta. Distribution maps were prepared to illustrate the total density, the number of species and the six most numerous taxa, as well as abiotic parameters. The general distribution pattern has revealed that the greatest number of species and the highest densities are at the estuary mouth, decreasing towards its inner areas. However the temporal and spatial changes observed at the estuary mouth have clearly shown the impact of environmental variations such as nutrients and freshwater input, attributed to increased rainfall in March. The increased flow in the Cananeia Sea, coming from the drainage basin, produces major changes in sediment and faunal composition. Ordinary kriging associated with Poisson modeling has proved to be a powerful and promising tool for modeling the macrofauna, despite the fact that it is not frequently used due to the scarcity of appropriate software.