You shouldn't use water as a solvent on gc.
Having said that, I was forced to use it on some samples by a non-technical manager.
The few samples I ran (say 20) didn't seem to hurt the instrument or the column. The chromatography was very poor. We had to retest with a liquid/liquid extraction, which drastically improved the results. The column being used was a capillary HP-5, 30 meter, microbore. The detector was mass spec, with an extended solvent delay time set.