Metabolomic footprinting, or exometabolomics, seeks to describe the complex chemical space surrounding cells. However, metabolite detection is hampered by negative matrix effects, especially when samples originate from high salt-content environments. We propose a sample preparation method for the untargeted exometabolomic analysis of seawater by gas chromatography-mass spectrometry. By investigating the independent effects of salt and water on metabolite ionization, we demonstrate residual water locked within salt crystals inhibits compound detection. Our novel preparation protocol includes a combination of solvent drying and ultra-sonication to facilitate the removal of water molecules form the salt palette and extraction of small molecules into the derivatization reagents. We can now detect a broad range of sugars, sterols and amino and organic acids from as little as 0.5 mL of seawater in the \u00b5M range. To demonstrate the utility of our approach, we monitored the exo-metabolome of Marinobacter adhaerens, a common marine bacterium during its exponential growth phase. With our untargeted method, we show M. adhaerens preferentially metabolizes glutamic acid and proline before valine, isoleucine and leucine. Our novel untargeted footprinting approach advances the capacity to detect small compounds from high salt content samples by filling a gap in analytical chemistry for the GC-MS analysis of marine samples.