Phytoremediation is considered a viable and cost effective emerging technology to clean-up trace elements. This approach has not been fully commercialized due the existence of various concerns about it. Those can be summarized as the uncertainty of the system behaviors at different scenarios, such as: contaminant, contaminant concentration and the behaviors of the physiology in the plant. Previous approaches have implemented diverse mathematical algorithms to characterize phytoremediation systems, such as: differential equation solution sets, statistical correlation and system dynamics approach. Phytoremediation Dynamic Model (PDM) employed the classical plant structure to simulate plant-soil-pollutant interaction. This model has proved its capability to mimic phytovolatilization processes of mercury chloride, obtaining more than 95% of correlation between the experimental data, and also provides the capability to know the contaminant flow rate and its concentration in plant tissue. The differential equations system which describes the model includes a comprehensive parameter which encapsulates plant bioavailability dependence in the contaminant-media interaction as a novel approach because this has not been found on the literature previously. PDM has proved the ability to mimic plant response as a function of contaminant concentration and the applicability as an assessment tool for phytoremediation system performance.