Abstract: Microcomputer software was developed to provide design and operational guidelines for development of commercial rhizofiltration systems, a phytoremediation process that uses plants to remove heavy metals from contaminated waters. A process model based on the Michaelis Menton equation was developed to quantify the ability of plants to accumulate and remove toxins within the rhizofiltration system. A series of algorithms process and incorporate this information with a system model of the rhizofiltration facility. The system model couples physical components of the phytoremediation system plant nursery, the rhizofiltration system, pre and post treatment of water, and post harvesting of plant biomass with engineering aspects of system design including processes, operations, facilities, and system integration. An engineering economic analysis tool within the software allowed for analysis of the impact of critical design variables on system efficiency.