The field of metabolomics aims to develop and apply methods to study the full complement of endogenous small molecules in biological systems. One of the major challenges in metabolomics is obtaining adequate resolution of compounds with similar physicochemical properties. The resolution of polar metabolites can be exceptionally problematic as these compounds are often poorly retained with reverse phase matrices. Here, we describe an advanced chemoselective tagging strategy to enrich and profile highly polar metabolites. Metabolite-reactive tags were appended with a hydrophobic p-Cl-phenylalanine residue, which conferred enhanced retention and resolution upon labeled small-molecules. Notably, the increased resolution afforded by hydrophobic tags minimized overlap in tandem mass spectrometry profiles for polar metabolites, thereby facilitating their structure determination in complex biological samples. Additionally, the chlorine atom of the tag permitted the discrimination of tagged metabolites from background peaks (i.e., false positives) and the discovery of metabolites that possess multiple copies of the same functional group. These studies designate chemoselective small-molecule tags as versatile tools for enriching and profiling challenging fractions of the metabolome.