In 2019, Taiwan completed its first thorough heavy metal investigation of irrigation canal sediments by this study with the support of Taiwan Environmental Protection Administration. Box-and-whisker plots were used to analyze the sediment distribution and to define metal concentrations. Possible metal pollution sources, the polluted agricultural land, irrigation area, and water sources were also evaluated using spatial analysis to understand the possible causes of sediment pollution. Results showed that the main heavy metal in agricultural land was Cu, found in 77% of contaminated agricultural land sites. Most sites with Cu pollution in sediments were in Taoyuan City and Changhua County. The heavy metals present in the sediment pollution sites in Taoyuan were consistent with those of possible pollution sources upstream, namely, Cr, Cu, and Pb. The main heavy metals in sediment pollution sites in Changhua were Cr, Cu, Ni, Pb, and Zn, whereas those for the polluted agricultural land sites were Cr, Cu, Ni, and Zn, without Pb. The main irrigation water sources in Changhua include drainages and rivers, with some receiving most wastewater pollution mass of release of Changhua, and functions as an irrigation water source with a high release mass in Cr, Cu, Ni and Zn. These findings indicate that the sites of sediment pollution, sites of polluted agricultural land, and the sources of pollution share corresponding heavy metal characteristics. Therefore, in Changhua, the sediments were polluted mainly because (1) the irrigation canals received the highest masses of pollutant releases into drainage wastewater of the county; and (2) the return flow from irrigation and the illegal discharge of wastewater. The preliminary assessment results for sediment pollution in Taoyuan also suggest that the main causes may be irrigation by polluted rivers or drainages and return flows.