Functional groups of phytoplankton make possible various classifications among taxa and this approach has been receiving a growing scientific interest. We compared three frequently used classifications as possible ecological tools in providing river zones along the large, Continental Atlantic River Loire. The different number of functional groups in each classification was synchronized into six clusters using the Self Organizing Map (SOM) method, which clusters (as river zones where relevant) were then compared in their response to geographical location, hydrological and chemical constraints.Our findings demonstrated that all the three classifications might serve as a rational tool, but at different level of understanding. Only approaches based on fine functional resolution in benthic and planctonic diatoms, as well as in cyanobacteria were able to provide reliable river zones at both whole river, and at spatio-temporal scales. Functional groups of these approaches followed different regional patterns in geographical, physical and chemical constraints, and were useful ecological indicators of natural river longitudinal processes, as well as of human impacts such as damming or agriculture