We investigate a relationship between geological history, groundwater flow paths and the spatial distribution of arsenic in aquifers of the upper part of the Red River delta in Vietnam. Hydrogeological conditions in the research area are complex. The fining upward sequence of Pleistocene alluvial sediments was partially eroded during the Holocene and covered by sand and clay deposited in fluvial environments. Sedimentary processes lead to the development of two flow systems. Shallow groundwater discharges either to the local surface water bodies or, in the areas where low permeable sediments isolating Pleistocene and Holocene aquifers were eroded, to the deep groundwater flow system discharging to Red River. Previously reported pattern of arsenic groundwater concentrations decreasing with an increasing sediment age is modified by the observed flow regime. Connection of the younger and older river channels resulted in a transport of high arsenic concentrations towards the Pleistocene aquifer, where low arsenic concentrations were expected.