If you extract bioactive compound (ethanolic extract) in the pure form, then you can directly prepare the nanoparticles from it. There are several papers are available where the NPs were synthesized from plant extracted bioactive compounds.
The conjugation of bioactive compounds with NPs can be characterized by FTIR, XRD etc.
I guess your intention is to immobilize the bioactive compound on the nanoparticle. Since it is soluble in water, I assume you are using some sort of organic nanoparticle. I would suggest checking the surface chemistry of your NP and compound for surface immobilization or encapsulation if you are targeting sustained release.
The details you have given in your question are too few and too vague; maybe if you give more details you might get some specific answers.
I isolated linalyl acetate from a herb using ethanol. I synthesized a nanoparticle which has free C=O group and it is now aavailable as a lyophilized powder. My doubt is if I incubate the ethanolic extract and the lyophilized nanoparticle, will it get immobilized automatically using the free C=O group?