The Water Framework Directive (European Council 2000) has to be applied to both the European continental area and to some EU overseas territories of EU member states. The present talk concerns the French Carribean Islands (Martinique and Guadeloupe). For such territories with a strong biogeographical specificity, biological indexes set-up and validated in continental Europe may not work satisfactorily. The main problems encountered result from particularities of geochemical and climatic conditions, as well as of taxa and their ecology. At the request of Water Offices, of the local services (DEALs) of the Environment Ministry of Martinique and Guadeloupe and the French National Office for Water and Aquatic Environments (ONEMA), a scientific consortium composed of ASCONIT Consultancy and IRSTEA performed a five year study based on a network of monitoring sites and other particular sites. The study aimed to: 1) describe abiotic environmental condition of rivers in situ (physico-chemistry, chemistry, descriptors of ecological ambiance like shading, flow velocity, depth...); 2) identify and count relative abundances of diatom taxa; and 3) set-up a new diatom index dedicated to the French West Indies, based on local relationships between abiotic descriptors and species ecology: the “Indice Diatomique Antilles”(IDA). The five-year study allowed the collation of 607 samples of diatoms and environmental measurements, obtained from 130 sites during seven field campaigns covering two different seasons. The main task was to identify and count the species in this little-known taxonomic context. Among the 512 different taxa observed, 178 have been found in sufficient numbers to establish their ecological profile and integrate them in the new index. Pollution being highly diluted because of the mountainous local context and the tropical climate, we chose to take into account only 47 “alert” taxa that are associated with significant anthropogenic alteration. Compared to a first version of IDA, a refined interpretation of their profiles allowed us to partition them into 25 "Taxons-", indicating average anthropogenic alterations and 22 "Taxons2-", associated with (?) severe pollution that reduce more strongly the index’s values. The new index version gives satisfactory results for quantifying the anthropogenic impact, which will be discussed. A ecological status assessment system for West Indian rivers, based on Equivalent Quality Ratios (EQRs) per natural zone, is currently being published at the French Official Journal.