A novel methodology called dynamic contaminant transport computational architecture (DCTCA) is developed to help flexibility of constructing process structure for radiological assessment of ecological systems. The method tracks radionuclide movements in ecological systems by doing calculations on vectors and matrices. All environmental components in an ecosystem are both sources and receptors as they are media that pass radionuclides. The transport factor matrix is the transformation matrix from sources to receptors. The cubic transport model base (CTMB) in the architecture allows a number of transport models to be selected and applied to a single source-receptor transport process. CTMB stores those models in a cubic structure and has them available to be selected and form a combined model set to be used in scenarios.