A framework was developed for the complementary use of mathematical models and microcosms in environmental assessment. A part of the framework was the use of microcosm data to define important ecological processes, including the mathematical functions and their rate coefficients, for inclusion in the mathematical model. As a case study, a mathematical model developed previously for the ecological assessment of power plant impacts was adapted to simulate the experimental conditions of a microcosm. Results indicated that ammonium absorption from the air was an important process for the microcosms but was not included in the simulation model. In most environmental situations, this is not an important process for simulation. The rate coefficients, compiled from the literature and used in the model to date, were generally applicable to the microcosms. Use of the mathematical model to anticipate results of microcosm experiments can help optimize the sample collection and analysis program necessary to meet the experimental design.