I am pleased to participate in the answer to your problem. I am a graduate of UM with PhD in 2013.
If you have water in your sample, you need to do GC-MS or GC-MSMS analyses. GC-FID is not suitable for water as you may know.
Additionally, Does your GC system involve a Headspace Sampler, or it is only a liquid sampler? A Headspace sampler uses heat with agitation on your sample's vial to evaporate the components of the sample and then withdraws the vapor cloud that results from the evaporation to inject it in the GC-MS. This technique is highly desirable when you have water in your sample. Water doesn't evaporate fast like many hydrocarbons do, and if you inject liquid sample that has a lot of water in it, water might not evaporate completely in the injection port and basically your analyses are not accurate at all.
I hope this is helpful. Reply here if you need more help.
Mukhtar gave a pretty good answer. However for small numbers of samples You will find that lots of columns stand water. (hundreds of sample is a different game).
I have done it every once in a while.
Cool down the GC as far as You can (25-30oC) inject by using split 1/50. If You do not get enough retention. Increase split ration and/or use a column with a thicker film.