Water contaminants play an important role in threatening amphibian species already in the midst of the sixth extinction. Species relying exclusively on agricultural habitats for breeding are under multiple, and sometimes synergistic, threats because of the high levels of contamination from chemicals used as plant fertilizers and pest control. In the Republic of Korea, two anuran species listed as endangered occur primarily in rice paddies: Suweon Treefrogs (Dryophytes suweonensis) and Gold-spotted Pond Frogs (Pelophylax chosenicus). The purpose of this study was to describe the relationship between the occurrence of these two species and water contaminants in rice paddies. Water quality and contaminants were assessed through multisite triplicate sampling. The rice paddies where the two anuran species occurred were characterized by higher concentrations of iron and lower concentrations of phosphate than rice paddies without the two species. Furthermore, low conductivity in the water was correlated to the occurrence of P. chosenicus, and low ammonium nitrate was a reliable predictor for the occurrence of D. suweonensis. These contaminants principally result from the application of chemical treatments on agricultural fields. The decline of these two endangered anuran species might be related to current agricultural practices.