Weathering of arsenic-bearing rocks in the Himalayas has resulted in the transport of sediments down the major river systems such as the Brahmaputra, Ganges, Red, Irrawaddy, and Mekong Rivers. For the past few thousand years, deposition of these sediments within the river basins during monsoonal flooding has produced profiles grading from surficial clay to deeper sands. Groundwater in the basins commonly has arsenic concentrations exceeding the World Health Organization's recommended drinking water limit (10 µg/L) by more than two orders of magnitude. Understanding the reason(s) for these elevated concentrations of arsenic within the sediments of Southeast Asia has remained a challenge, owing to the complex biogeochemical and transport processes within the soils and sediments. Complex sedimentary stratification (e.g. clay and sand lenses which vary in thickness and depth) and shifting groundwater dynamics during seasonal, wide swings in hydrologic flow regimes create a convoluted system where resolving the processes controlling arsenic concentrations in aquifers are challenging. We examined specific pathways of arsenic release (desorption/dissolution mechanisms) within these soils and sediments, inclusive of iron, arsenic, or sulfur reduction, and identified downward hydraulic gradients which carry arsenic to the subsurface, providing a specific scheme of arsenic release and transport to underlying aquifers. We utilized a suite of field measurements, intact core leaching experiments, sediment incubations with native microbial communities, geophysical measurements, and advanced micro-spectroscopies to elucidate the biogeochemical reaction pathways controlling arsenic release and transport. Our results demonstrate that arsenic is released within near-surface (<4 m) sediments during the onset of reducing conditions, and that transport to the subsurface, and hence deeper aquifers, is evidenced by preferential flow pathways and near-surface zones of hydraulic conductivity conducive to the downward transport of arsenic.