This study shows the analysis of several commercially available coconut water products using a GC/MS system equipped with a versatile autosampler and sample preparation robot capable of performing a wide range of standard sample introduction techniques including thermal desorption. A fast and efficient analysis method based on stir bar sorptive extraction (SBSE) in combination with thermal desorption -GC/MS was developed for the determination of flavor compounds, pesticides, antioxidants, compounds migration from packaging materials, and off-flavors in coconut water.