Diatoms are mostly aquatic plants, growing in various environmental conditions and habitat. Because of their high sensitivity to environmental variations and rapid response to degradation, they are used as biological indicators. This study aimed to analyses the physicochemical parameters and diatoms assemblages of waterfalls. This will allow determining the key environmental factors that are responsible for both diatoms and Podostemaceae spatial and temporal distribution in the studied area.Water and diatoms samples were taken respectively for the physicochemical and biological analysis. Diatoms samples were collected by scraping the bedrocks and submerged plants; diatoms were subsequently identified to the species level using a light microscope. For physicochemical data analysis, a principal component analysis approach was used while diatom’s data were submitted to a correspondence trophic analysis. A total of 169 diatom species were identified in both waterfalls. Podostemaceae poor waterfalls were more species-rich (127) than the rich ones (110). Podostemaceae poor and Podostemaceae rich waterfalls were characterized with low mineralization, low values of pH and oxygen saturated water. The observed assemblages were composed of oligotrophic to eutrophic species, acidophilic, neutrophilic and high to moderate oxygen saturated water taxa. The ecology of different species revealed that dissolved oxygen was the main parameter which controls the distribution of diatoms, and probably the Podostemaeceae one in the two type of waterfalls Podostemaceae poor waterfalls are characterized by Fragilariacapucina and Gomphonema gracile. Podostemacea rich waterfalls were characterized by Eunotiafaba, Eunotiarhomboïdea, Pinnularia microstauron, Gomphonema procerum and Gomphonema clavatum.