It is not advisable to run water soluble plant extract directly In HPLC. It can damage the Column. You can follow following steps for your sample.
The brief steps are:
First of all you isolate the pure fraction from plant extracts using following techniques. First run TLC to know the type of fractions. After that Column Chromatography with HPLC, after isolated pure fraction run FT-IR, LC-MS, HNMR, CNMR for structure elucidation. You can read my papers too.
Depending on the HPLC column you can run the aqueous samples there are stationary phases which are particular for the separation of polar analytes such as C16 functional group bounded to silica. To do away with that use any polar solvent. You can use 100% methanol or may reduce its percentage to 80% depending on the retention time and peak of the compound that you are getting.