Dioxane migrates in groundwater with low sorption, low degradation, and low volatilization according to its physicochemical properties. 1,4-Dioxane migration therefore strongly depends on groundwater flow. Hydraulic conductivities, the most uncertain parameters and critical to groundwater flow, should be precisely determined. In a conventional approach, groundwater flow is estimated by calibration to optimize hydraulic conductivities, and then the calibrated groundwater flow is used for predicting 1,4-dioxane distribution considering other parameters such as source location and concentration. Although other parameters are properly set, 1,4-dioxane distribution cannot be always precisely predicted because the calibrated groundwater flow model does not perfectly present the real groundwater flow. Thus, the calibrated groundwater flow should be reevaluated to define the most suitable hydraulic conductivities considering 1,4-dioxane distribution. This study proposes a new approach with verification process of groundwater flow estimation for precisely predicting 1,4-dioxane distribution in groundwater. In this approach, several acceptable sets of hydraulic conductivities in term of groundwater heads are estimated by calibration and each groundwater flow is verified to match between calculated and observed 1,4-dioxane concentrations. The effectiveness of our new approach comparing to the conventional one was proved by a case study at an illegal dumping site in Japan where three aquifers have been contaminated by 1,4-dioxane for about 15 years. Eight acceptable sets of hydraulic conductivities of the three aquifers were determined by calibration using observed groundwater heads, and then verified to minimize the errors in 1,4-dioxane concentration. As a result, 1,4-dioxane distribution was predicted by our approach more precisely than the conventional approach.