Boron compounds play a crucial role in various industries, and accurate quantification of boron is essential for quality control and environmental monitoring. This study presents a simple, rapid, and reliable method for determining boron in aqueous solutions using suppressed ion chromatography coupled to electrospray ionisation-triple quadrupole mass spectrometry (IC-ESI-QqQ-MS). Boric acid (B(OH)3) was retained as the tetrahydroxyborate ion (B(OH)4−) on a CarboPac PA300-4 μm anion-exchange column using isocratic elution with 40 mM KOH. During the neutralization process at the suppressor, B(OH)4− was converted to B(OH)3, which subsequently generated the metaborate ion [BO2]− (m/z 43) within the electrospray ionisation source. By employing a pseudo-selected reaction monitoring (SRM) transition from m/z 43 to m/z 43, the method achieved a limit of detection (LOD) of 2.45 μg/L of boron, the lowest reported in the literature to-date for an IC-based method. The analytical performance of the method demonstrated no carry-over issues, no matrix interferences, and excellent intra- and inter-run repeatability of 2.03% and 3.41%, respectively. The method was applied to the evaluation of boron uptake and retention by Tasmanian Oak timber blocks, treated by dip-diffusion in a boric acid solution of 2.5% Boric Acid Equivalent (BAE, m/m) under controlled laboratory conditions. Quantitative determination of the retained and unretained boron allowed a mass balance evaluation and confirmed the accuracy and reliability of the method, with recoveries ranging from 99.3% to 100.2%.