Small Shallow Lakes (SSL) support exceptionally high and original biodiversity, providing numerous ecosystem services. Their small size makes them especially sensitive to anthropic activities, that causes a shift to dysfunctional turbid states and induces loss of services and biodiversity. In this study we investigated the relationships between environmental factors and macrophyte communities. Macrophytes play a crucial role in maintaining functional clear states. Better understanding factors determining the composition and richness of aquatic plant communities in least-impacted conditions may be useful to protect them. We inventoried macrophyte communities and collected chemical, climatic and morphological data from 89 least-impacted SSL widely distributed in France. SSL were sampled across four climatic ecoregions, various geologies and elevations. Hierarchical cluster analysis showed a clear separation of four macrophyte assemblages strongly associated with mineralisation. Determinant factors identified by db-RDA analysis are, in order of importance, geology, distance from source (DIS, a proxy for connectivity with river hydrosystems), surface area, climate and hydroperiod (water permanency). Surprisingly, at country-wide scale, climate and hydroperiod filter macrophyte composition weakly. Geology and DIS are the major determinants of community composition, whereas surface area determines floristic richness. DIS is identified as determinant in freshwater lentic ecosystems for the first time.