Contaminated soils and waters pose a major environmental and human health problem, which may be partially solved by the emerging phytoremediation technology. This cost-effective plant-based approach to remediation takes advantage of the remarkable ability of plants to concentrate elements and compounds from the environment and to metabolize various molecules in their tissues. Toxic heavy metals and organic pollutants are the major targets for phytoremediation. In recent years, knowledge of the physiological and molecular mechanisms of phytoremediation began to emerge together with biological and engineering strategies designed to optimize and improve phytoremediation. In addition, several field trials confirmed the feasibility of using plants for environmental cleanup. This review concentrates on the most developed subsets of phytoremediation technology and on the biological mechanisms that make phytoremediation work.