In this study, a compact capillary liquid chromatography (capLC) system (<10 Kg) has been coupled with two small-footprint and portable single quadrupole mass spectrometers (<35 Kg) for the analysis of haloacetic acids (HAAs) in water samples. The portable capillary liquid chromatograph was equipped with a polar-modified C18 column (100 × 0.5 mm, particle size: 3 μm) and utilised gradient elution with 0.05 % formic acid and methanol to selectively separate and quantify the 9 HAAs (HAA9) recommended for monitoring by United States Environmental Protection Agency (USEPA). The successful quantification of HAA9 was accomplished using a portable capLC-ESI-MS system with a single quadrupole mass analyser for the first time without the addition of ion-pairing agents. Direct injection was applied to analyse HAA9 in tap and swimming pool water using the system incorporating the Shimadzu LCMS-2050 mass spectrometer. The limits of the detection (LODs) attained using the capLC-MS system were below the maximum contamination level (MCL), 60 µg/L, set by USEPA for the five most common HAAs in drinking water (HAA5). Dichloroacetic acid (DCAA) was detected in local tap water at the level of 5.3 µg/L, while 142.4 µg/L and 311.4 µg/L of DCAA and trichloroacetic acid (TCAA), respectively, were determined in local swimming pool water. The small-footprint capLC-MS system is compatible with the on-site analysis within water treatment plants and provides a cost-effective and green solution for the quantification of HAA9.