The aim of this research was to investigate possible phenotypic variation profile of Marsilea crenata Presl. cultivated in water and in the soil, to find alternative cultivation techniques to fulfill the increasing demand for pollutant-free plants. Phenotypic profile was investigated through macroscopic and microscopic examinations of all plant parts, and phytochemical screening on the ethanol extract of the leaves using thin layer chromatography technique was conducted to detect the terpenoid constituents. Results showed a variation of phenotypic profiles in the macroscopic examination caused by different cultivation methods. Phytochemical screening showed spots of terpenoid compounds with different color intensity. No differences were found in the microscopic examination of the leaves, petioles, and stems. Since major profile changes did not occur, M. crenata is recommended to be cultivated in water as its original habitat by providing a better caring and quality of water. Due to its phytoremediation property, it is necessary to grow M. crenata in pollutant-free water.