Similar to many southern and southeast Asian regions, the mobilisation of arsenic (As) from sediments has driven a widespread contamination problem for groundwater resources in the Cambodian Mekong Delta. For the first time, the seasonal changes in As concentrations and potential links to groundwater pumping for irrigation in shallow aquifers of the Cambodian Mekong Delta are investigated. Using environmental tracers (δ18O, δ2H, 3H, major/trace ions and rare earth elements) the natural and pumping-induced changes in hydrogeological processes are identified. Three conceptual models are proposed: Model 1, where there is limited local recharge or low recharge rates (3H mean residence time > 60 years) and groundwater has a large range in As concentrations (0.2 to 393.8 μg/L). In this semi-confined aquifer, only one of the six groundwater sites has As concentrations that increase (by 10.9 μg/L) potentially due to groundwater pumping and resultant mixing with high-As and low (Pr/Sm)NASC groundwater. However, data on groundwater extraction volumes is required to verify the link with irrigation practices. Model 2, where groundwater is recharged by evaporated surface waters (fractionated δ18O and δ2H). There are moderate As concentrations (64.1–106.1 μg/L) but no significant seasonal changes even though the recharging waters have relatively greater organic carbon contents during the dry season (reduced Ce/Ce*anomaly). Finally model 3, where groundwater is significantly recharged by wet season rainfall (~50% from δ18O data). There is a minor increase in As concentrations with recharge (by 6. μg/L). These combined results highlight an aquifer system in the irrigated region of the Cambodian Mekong Delta where As concentrations are largely impacted by natural rather than irrigation processes. Seasonal-scale recharge processes control As processes where the aquifer is not confined by shallow clay layers, and where the aquifer is semi-confined As concentrations largely reflect longer-term natural processes.