Contaminants found in the soil and in the atmosphere frequently find their way into plants. Because plants are at the bottom of the food chain, analysis of this pathway contributes to health risk assessment studies. On the other hand, plants that exist at a contaminated site have a potential effect on contaminant transformation and migration within the soil or the atmosphere. In this study, a modeling framework was developed to integrate the plant pathway into soil contaminant transport models. A soil–plant system model was developed by coupling soil moisture distribution, contaminant transport, plant life cycle, and plant pathway models. The outcome unifies single-medium continuous models with multimedia compartmental models in a flexible framework. The framework recognizes that plants are dynamic biologic systems that regulate their life cycle in interaction with existing conditions in the ambient environment, which significantly influence the dynamics of the overall complex system. The model developed was applied to a hypothetical contamination scenario where the effect of plants on contaminant migration within the system was investigated. Also, the outcome of the plant pathway as it responds to water flow and contaminant transport dynamics was analyzed. A mass balance analysis found that the processes of volatilization and root water uptake are very critical in determining the contaminant fate within the system. A sensitivity analysis showed that the contaminant concentration within the plant is significantly affected by the variation in the values of the retardation factor, transpiration stream concentration factor, and contaminant half-life within the plant. The outcome of these applications reflects the effect of multiple levels of complexity associated with plant growth and root water uptake representations within the soil.