There are some discussions about water injection on Restek's site (the Blog). The most information I've been able to find is from clinical labs. Possible problems:
Injection: as little as possible due to water's expansion. Also the problem of everything else in the sample deposited on the liner/column. Must use glass wool to aid evaporation.
Column: water doesn't destroy the column, but the phase must be matched to water's polarity, ie wax type column or possibly blood alcohol column. Also, carrier gas should be high purity regardless the application.
Detector: I haven't seen any problems, unless using a nonpolar column, the water beads up below about 80 degrees and can put out the flame.
I have had best results mixing the water sample 1:1 with an alcohol, peak shapes and calibration much better.
Good luck, and any way to avoid water the better.