In this study the Water Quality Analysis Simulation Program (WASP7) was used to evaluate the transmission of hexavalent chromium (Cr(VI)) contamination in a water–sediment system and its flux into cultivated soils. The agricultural areas adjacent to the Wu River in Taiwan were taken as the study area, as these soils were found to be heavily polluted with Cr(VI) concentrations of 3,271–16,799 μg/kg. It was found that the rates of accumulation of Cr(VI) are affected by the distance from the source of contamination and the size and type of cultivated areas. Specifically, maximum concentrations of Cr(VI) most rapidly accumulated in the smallest cultivated areas. The highest concentrations of Cr(VI) (4.27 mg/kg) were detected in soil from Changhua city, and correlated with the greater risk of gastric cancer in residents from this area. Specifically, the risk of gastric cancer due to Cr(VI) contamination of agricultural soil was 3X10-7-15.2X10-6 in Taichung city (upstream) and 1.3X10-6-76.3X10-6 in Changhua county (downstream). More worryingly, young children had a threefold greater risk of gastric cancer than adults. The values of statistical life-years (VSLYs) were US$6.2–10 million for rice, US$42–60 million for corn, and US$360–580 million for other vegetables, respectively, each year. It is critical that techniques other than source reduction are used to reduce health costs associated with human exposure to Cr(VI), such as chemical oxidation or ion-exchange treatment to remove Cr(VI) from factory wastewaters, prior to their discharge into rivers.