Microbially mediated reductive processes involving the oxidation of labile organic carbon are widely considered to be critical to the release of arsenic into shallow groundwaters in South and Southeast Asia. In areas where there is significant pumping of groundwater for irrigation the involvement of surface-derived organic carbon drawn down from ponds into the underlying aquifers has been proposed but remains highly controversial. Here we present isotopic data from two sites with contrasting groundwater pumping histories that unequivocally demonstrate the ingress of surface pond-derived organic carbon into arsenic-containing groundwaters. We show that pond-derived organic carbon is transported to depths of up to 50 m even in an arsenic-contaminated aquifer in Cambodia thought to be minimally disturbed by groundwater pumping. In contrast, in the extensively exploited groundwaters of West Bengal, we show that pond-derived organic carbon is transported in shallow groundwater to greater depths, in excess of 100 m in the aquifer. Intensive pumping of groundwaters may potentially drive secular increases in the groundwater arsenic hazard in this region by increasing the contribution of bioavailable pond-derived dissolved organic carbon drawn into these aquifer systems and transporting it to greater depths than would operate under natural flow conditions.