Over the past decade, Europe's Water Framework Directive (WFD) has prompted a large amount of ecological research aiming at establishing river typologies and ecological indicators in member States. Yet, the lack of robust bioindicators in Europe's overseas regions arguably reflects minimal knowledge of the distribution patterns of aquatic species in the Community's outermost areas. Specifically, there has been no published classification of rivers for any European overseas region. Fifty-one sites were sampled for benthic invertebrates and environmental variables (land-cover, physical habitat, and water chemistry) in Guadeloupe, French Lesser Antilles. Redundancy analysis and k-means clustering were used to bring out spatial patterns in species composition in relation to environmental conditions. Our results highlighted the importance of land cover and geomorphology in delineating three ecological sub-regions (clusters) for freshwater invertebrates. Deviation from predictable community structure only occurred when river sites were subjected to harsh water chemistry alterations (urban runoff, wastewaters). Changes in species richness did not detect environmental stress efficiently within a given sub-region, probably because most sites are naturally species-poor due to the insular context and/or because disturbance is often weak. However, differences existed between clusters in terms of species identity and numerical dominance. Our a posteriori typology of sites was compared to local a priori expert opinion of river health, in an attempt to better characterize the network of survey sites, and to target sites for reference conditions.