Understanding the biogeochemical behaviour of arsenic in the weathering and shallow subsurface environment depends critically upon determining the nature and distribution of the chemical species present in natural waters. To this end, coupled ion chromatography-inductively coupled plasma mass spectrometry (IC-ICP-MS) is widely used, though species fractionation during ultrasonic nebulization, and matrix-dependent ionization in the plasma are analytical issues that need to be addressed. Hexapole collision cell technology is shown to be effective in suppressing chloride-based polyatomic interferences. Irrespective of the analytical technique used, As(III)/As(V) ratios of natural waters may change substantially during storage due to (1) differential adsorption of arsenic species on hydrated ferric oxides (HFOs); and (2) microbial activity. A wide range of apparently contradictory speciation changes observed by various workers can be rationalized in terms of the differences of microbial consortia present in different water samples. Arsenic speciation in certain water types can be stabilized for days or even weeks by combined filtration, acidification and refrigeration whilst the addition of EDTA and the use of 0.1 μm filters is indicated for iron-rich waters and waters with high activities of redox-active bacteria, respectively. Although the use of hydrochloric acid has been reported elsewhere as resulting in the apparent oxidation of As(III), we show that for certain water types it acts as an extremely effective preservative of arsenic speciation.