In general, you would never inject water into a GC-MS as it would damage most columns. Also, samples should be run in either the solvent they were extracted in or a very similar solvent to make sure that they dissolves properly for the analysis. So always solvent extracts for GC-MS.
Never use water in the GC MS which is gas chromatography which is used for the volatile compunds such as essential oils, while the LCMS can be used for nonvolatile compounds.