Dissolved organic matter (DOM) is linked to the heterogeneous distribution of elevated arsenic (As) in groundwater used for drinking and irrigation purposes, but the relationship between DOM characteristics and arsenic mobility has yet to be fully understood. Here, DOM from groundwater sampled in the Bengal Basin region was characterized using both conventional bulk emission-excitation (EEM) spectroscopy and high-performance size-exclusion chromatography coupled to spectroscopy (HPSEC-EEM). Notably, application of the novel HPSEC-EEM approach permitted the total fluorescence of individual samples to be independently resolved into its underlying components. This allowed the external validation of the bulk-sample fluorescence decomposition and offered insight into the molecular size distribution of fluorescent DOM. Molecular size distributions were similar for the UVA fluorescent (C310 and C340) as well as the three visible fluorescent (C390, C440, and C500) components. There was a greater visible fluorescence in shallow aquifer samples (10-33 m) with high As (SH, up to 418 μg/L) than in samples from the same depth with lower As (up to 40 μg/L). This indicated a link between DOM quality and As mobility within the shallow aquifer. The deep aquifer samples (170-200 m) revealed DOM characteristics similar to SH samples but had low As concentrations (<4 μg/L), signifying that the deep aquifer is potentially vulnerable to As contamination. These findings pave the way for a more comprehensive assessment of the susceptibility of drinking water aquifers, thereby supporting the management of groundwater resources.