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Many studies in marine coastal lagoons have focused on the marine-to-terrestrial gradient as a main source of variation for the structure of assemblages. In this paper, the magnitude of differences among locations arranged along the marine-to-terrestrial gradient of the western lagoon of Orbetello (Grosseto, Italy) was contrasted with the amount of spatial variability occurring among sets of locations that were not positioned along this axis. We propose that if the most important processes influencing assemblages were those associated with the external–internal gradient of the lagoon, as usually supposed, then assemblages should differ more among these locations than among any other locations. To test the above proposition, four locations arranged along the two major axes of the lagoon were established in November 2000. Each location was sampled three times (November 2000, April 2001, August 2001) to test for temporal consistency in spatial patterns. At each time of sampling, three replicate sites were established in each location. This design enabled estimates of spatial variability to be obtained at three scales: among locations hundreds of meters apart, among sites tens of meters apart and among quadrats hundreds of centimeters apart. Non-metric multidimensional scaling (nMDS) ordination plots on abundance data revealed differences among assemblages hundreds of meters apart. Assemblages in the inner part of the lagoon were separated from those closer to the sea inlet, depending on the marine-to-terrestrial gradient. In addition to this pattern, differences also occurred among assemblages hundreds of meters apart, but positioned at a similar distance from the sea. Multifactorial Anovas on abundance of the most common taxa showed significant differences in mean values at the scales of location and site, with patterns changing over time. These results indicated that spatial structure in assemblages was not a distinctive feature of locations arranged along the marine-to-terrestrial gradient in the lagoon of Orbetello. Similar differences also occurred among other sets of locations at the scale of hundreds of meters, regardless of their position in the lagoon. [Copyright &y& Elsevier]