Rice is one of the most important staple foods worldwide. Soil contamination with heavy metals and food safety problems occur in many countries as a result of numerous human activities, particularly wastewater and solid waste disposal. This review paper provides a schematic summary of heavy metals in identification processes, transport in soil to different rice varieties, and soil remediation strategies and techniques surrounding the agro-environmental impact in paddy soils based on a description of Taiwan’s experiences and database. In terms of the soil control standard, heavy metals including As, Cd, Cr, Cu, Hg, Ni, Pb and Zn are regulated by the Soil and Ground Water Pollution Remediation Act of Taiwan. Owing to the heavy metal source from wastewater along irrigation systems, heavy metals not only accumulate in the surface soil (0–30 cm), but are also highly distributed at the main entrance of irrigation water into individual paddy fields. Moreover, sediments in the irrigation canal have to be dredged and the irrigation system needs to be isolated from the discharge system of wastewater to maintain soil quality. Cadmium in rice grains accumulates more significantly in Indica varieties than in Japonica varieties, and this accumulation exceeds the food quality standard. The best well-performing metal uptake models have been developed to predict Cd levels in rice grains for Indica and Japonica varieties using soil bioavailable Cd and Zn concentrations extracted by 0.01 mol L−1 CaCl2. Soil remediation techniques, including turnover and dilution, in situ stabilization by chemical amendments and phytoremediation, have been tested and recommended in Taiwan. Although the high background levels of As, Cr and Ni, which were higher the soil control standard in some paddy soils, are derived from andesite and serpentinites in Taiwan, rice quality and yield were not adversely affected by these metals when labile concentrations were very low. Overall, it is necessary to identify the bioavailability of heavy metals in different soil types from specific case studies to provide reliable parameters for health-based risk assessments and to further achieve the goal of food safety and sustainable agriculture.