This study is part of a wider predictive modeling work on benthic habitats along the Portuguese Continental Shelf. The aim here is to characterize the variability of the data collected by an acoustic ground discrimination system connected to a single-beam echo-sounder, considering different factors: the spatial survey step used to integrate the acoustic data (125, 250, 500, 750 or 1000m) and the sediment types. The surveyed area covered approximately 5400km2, with depth between 15 and 150m and superficial sediments ranging from fine gravel to mud. The acoustic survey followed 27 transects, perpendicular to the coast line, and 121 sediment samples were collected for ground-truth. The acoustic data integrated at 250m spatial step presented the lowest within sites variability and the highest among sites variance. Also, when the acoustic data was organized in groups according to the superficial sediment types, the 250m spatial step presented the highest variability among groups. Both results indicated that this spatial step should be used to integrate the acoustic data in future habitat modeling work.