In 2002, the Environmental Protection Administration of Taiwan began a detailed survey of heavy metals in soils, to determine the scope of the contaminated lands in the Changhua County’s agricultural fields. It was found that agricultural lands have been seriously polluted with Cr, Hg, Cu, Ni, and Zn, due to industrial wastewaters. This study, characterized the processes associated with heavy metal pollution by analyzing heavy metal contents in sediments within two periods, 2002 and 2010. This study employed geostatistical and multivariate statistics to obtain spatio-temporal variations of heavy metal pollution in paddy fields. The results indicate that, changes in industrial types have been altered the characteristics of pollutions, such as reducing the number of plants in industries (i.e., electroplating, surface treatments, metal works, chemicals, papermaking, etc.). Their wastewaters contained a large number of Ni, making the pollution composition of driven factors have been changed that can be indicated in this study. Pollution distribution and irrigation systems are positively correlated and concentrations of Cr, Cu, Ni, and Zn were inversely proportional to the scale of irrigation channels.