We used different solvents for extractions of medicinal plants. There are various techniques such as TLC, HPLC etc used for separation of mixture of compounds, but I how tol isolate water soluble compounds?
Keep your extract well preserved because water extract catches fungus very often if kept without proper drying. Better, spray dry your extract.
If you want to isolate compounds from the extract, first do chromatography and find out what chemical compounds are present. Mostly you will find sugars and proteins in water. Polysaccharides are very important constituents in many cases and they are bioactive also. It depends upon the plant and its chemical constituents.
So once you know about the nature of compounds present, try to isolate them through column or prep TLC. For TLC of water extracts, mostly Butanol: Acetic Acid : water (4:1:3) is used, so you can also try this and its variants.
If you are only interested for water soluble compounds, to my understanding it has to be done without using significant amount of organic solvents. For example, I extract specific water soluble compounds by incubating the biological material at 45 degree for 2-3 hrs in 20-30% (v/v) methanol in water. I freeze-dry the resultant clear supernatant and re-constitute in water or buffer as per requirement. I also extract other specific water soluble compounds mostly proteins, by grinding or freeze-thawing the biological material in 50-75 mM phosphate buffer at pH 6.8-7.0. I freeze-dry the resultant supernatant and re-constitute in water or buffer as per future use.
After the extraction process, you have to concentrate the extract. To recover compounds, first let us know which compounds are of your interest, like tannins, sugars, proteins etc. As each compound has a different procedure it is important for us to know your compound of interest.