The new Water Framework Directive requires, thanks to stream communities: I) to describe the naturel expected conditions for all aquatic ecosystems (abiotic and biotic reference conditions), and then ii) to describe the ecological status of water bodies under anthropiogenic disturbance, by comparing to the expected conditions previously defined. In order to achieve the diatom communities collected at 49 undisturbed sites spread in the Adour-Garonne basin, South-western France. Environnemental factors known to be revelant in diatom assemblage structure were also considered. We used Self Organizing Maps to perform the analysis of community similarities between sampling sites.Our results showed 4 major groups of sampling sites based on their geochimestry.We concluded that for diatoms, and in the study area, the natural state could differ according to stream types. Using the Structuring Index, species were ranked according to their importance in this stream bio-typology.