I have a water sample with inorganic salts dissolved along with the interesting compounds. GC worked well with standard solutions of the compounds. Will the salts ruin the column?

Thanks in advance.

Inorganic salts deposits inot column and possible plug the column. It is not a good idea to inject samples with inorganic salts on GC column. However, you can try to have glass wool or OV-101 packed injector liner to filter salts out.
Good luck.

Just a reminder:
check FIRST if water can be injected directly on your GC column. Many stationary phases are fouled by it!

If you are using a heated split/splitless injector, the salts will be deposited in the liner as the water evaporates. They will change the nature of the liner's surface, leading to adsorption and possibly to degradation of labile analytes. Both phenomena will cause deterioration of the chromatography. If you use silylated glass liners, you cannot rinse the salts off the surface without destroying the deactivation chemistry. Monitor your chromatography and replace the liner when peak shape and height start a downward trend.

Bonded and crosslinked capillary columns will not be damaged by water injections per se. These columns can tolerate injections of any organic solvent or water without producing damage to the stationary phase. What will damage these stationary phases are inorganic acids and bases, and some of the perfluorinated acid byproducts of derivitization reactions using acid anhydrides.

Nonbonded phases can be damaged by injection of water and/or some organic solvents.

Often times it is assumed that water injections are damaging a bonded capillary column due to peak shape degradation after several injections are made. In these cases, it is not the water itself that is damaging the phase but rather the things dissolved in it that are producing what appears to be damage. Water will carry inorganic material which will deposit in the liner and front of the column. This material will cause peak shape degradation due to activity and/or flow path disruption. Actually, this material (assuming it is not an inorganic acid or base) does not damage the phase but just produces poor chromatography. Column cleanup can be accomplished by trimming the front of the column and/or backflushing with solvent.

Frequent front-end maintenance should help to avoid chromatography problems if required to inject "salty" samples. Change the liner and clip the front of the column often. A guard column may be advised if many samples are being analyzed. Also, glass wool in the liner may help to retain some of the nonvolatile salt material.

Silanised porapak Q is suitable for such analysis. The glass liner should be having some of the phase in it and it must be replaced daily. If peak shape is getting distorted after few injections, an injection of 2 Ul acetone helps in setting it right.
I am suggesting this because I have worked on effluent water analysis of toxicants on ppm level.