Industrialization, urbanization and intensive use of farm inputs can pollute agricultural areas. The study was then conducted to assess the levels of chromium (Cr), nickel (Ni), copper (Cu), cobalt (Co), zinc (Zn), arsenic (As), molybdenum (Mo), cadmium (Cd), mercury (Hg), and lead (Pb) in the country’s major rice areas. The study also determined the contributions of soil properties, land uses, irrigation water, and farm inputs to the metal levels. Strategic collections of soil, plant and water samples in the country’s major soil series planted to rice, analyses of samples using x-ray fluorescence or atomic absorption spectroscopy, and farmer interviews were done. Metal levels were very high in Zambales and Negros Occidental soils due to deposition or use of metal-enriched mine tailings and irrigation water. Soil metal concentrations in Zambales far exceeded the intervention values of 180 mg/kg for Cr and 100 mg/kg for Ni. Soil metal levels in Negros Occidental exceeded the intervention value of 190 mg/kg for Cu and Mo. Rice plants in Negros Occidental exceeded the toxic levels of 30 mg/kg for Cu and 10-50 mg/kg for Mo due to the very high soil Cu and Mo concentrations in the area. Molybdenum concentrations of rice plants in Sultan Kudarat and Camarines Sur exceeded the toxic level due to the high amounts of foliar chemicals applied at >66 sprayer loads per year. The study implies that rice areas deposited with mine wastes have high heavy metal levels, and foliar chemicals can increase metal levels in rice.