This study applied multivariate factorial kriging to derive the characteristics of the spatial variations of groundwater arsenic distributions at different scales on the ChiaNan floodplain, Taiwan. Seven variables (dissolved oxygen, oxidation-reduction potential, alkalinity, sulfate, iron cations, manganese cations and total organic carbon) and Arsenic were adopted to analyze the mechanisms of arsenic enrichments in groundwater. The hydrogeological environment had spatial and quantitative influences on arsenic enrichments at different scales. The regional scale was set to 32 km referring to the extension distance of flow paths to reflect the effects of flushing in the aquifer, while the local scale was set to 16 km referring to the farthest distance of seawater intrusion to determine the influence of seawater intrusion. The results of factorial kriging suggested that arsenic releases resulted partially from pyrite oxidation during the flushing at the regional scale and partially due to the siderite dissolution at the local scale. Overall, the alkalinity dominated arsenic distribution in groundwater at both the regional and local scales. The multivariate factorial kriging results also demonstrated that seawater intrusion slightly affected the increase of arsenic in groundwater, accounting for only 17.3% of total variation. However, the interaction of seawater intrusion and arsenic distribution in space indicated that seawater intrusion restrained the distribution of arsenic from the areas where seawater was located. High dissolved oxygen was found at where over-pumping induced drawdown cones occurred and also limited the spatial variation of arsenic. Our findings indicate that multivariate factorial kriging can be a useful mapping tool to improve understanding of the mechanism of arsenic release in groundwater at different scales. And the results conducted from the application of multivariate factorial kriging in southwestern Taiwan reveal the important influences of the hydrogeological processes, either artificial or natural, on the arsenic variations in groundwater.