Simple morphological traits of phytoplankton have proven to correlate well with the functional properties of taxa. A logical way of distinguishing functional groups of phytoplankton is to cluster species according to their morphological traits, instead of phytosociological traits, which are difficult to measure and incomplete for the vast majority of phytoplankton species. This novel approach inspired the establishment of morphologically based functional groups (MBFG) for lake phytoplankton. This study considers the MBFG as a potentially suitable tool for investigating and comparing the potamoplankton assemblages in riverine ecosystems. This study constructed a special version of MBFG that is aimed at rivers, termed MBFGR. MBFGR is based on information obtained from more than 800 samples of potamoplankton and zooplankton collected from 101 rivers located in four climate zones. Their habitat templates were also described by the thresholds of the environmental variables that promote group dominance. Despite its similar framework with MBFG, MBFGR emphasized the presence of flagella, size and shape, exoskeletal structures, life strategy and subdivision of diatoms. Their habitat templates are outlined by additional factors connected to hydrology and river types. Moreover, each discussed template includes consideration of grazing by zooplankton. Theoretically, MBFGR is better than MBFG because it can sensitively capture the ecological preferences of phytoplankton groups most associated with rivers and provides empirical values to reflect the environmental conditions in riverine ecosystems.