A water stationary phase is explored as a novel means of selectively separating unsaturated analytes in gas chromatography. Several unsaturated/saturated analyte pairs consisting mainly of carboxylic acids and alcohols were examined using both a 30-m conventional non-polar HP-5 column and an 11-m water phase column. For most investigated on the HP-5 column, analytes often eluted very close to each other (~ 6–12 s apart) with poor resolution. By comparison, the shorter water phase column well separated each of the analogue pairs by about 3–8 min or more. As well on the water phase, analytes with a triple bond were much more retained than those with two double bonds, which in turn were much more retained than those with one double bond. Conversely, on the HP-5 column these were poorly separated if at all. Additionally, cis/trans isomers were baseline resolved on the water phase but co-eluted on a 30-m conventional polar Carbowax column. Similarly, positional isomers varying the location of the double bond were found to separate with a selectivity value near 1.1 on the Carbowax column, whereas on the water phase column they yielded a value of 1.3 and eluted in the reverse order. Addition of various metal ion salts to the water phase was explored. While Ca2+ ion produced modest increases in selectivity, the addition of Ag+ ion was most influential and further increased the original water phase selectivity by a factor of 2.3. The mechanistic implications of OH–-pi bonding in the water phase was discussed as a potential origin for the selectivity observed. The method was applied to gasoline, essential oil, and food stuff analysis. Results indicate that this method could be a very useful means of selectively separating such unsaturated analytes.Graphical abstract