Ecological modeling of dynamic systems is used on various scales to gain a further understanding of syntheses and linkages. Ecological modeling can be used to describe system interactions of their interdependent parts linked together by exchanges of energy, matter and information. Integrative modeling techniques have been developed that allow for environmental decision-making of ecological engineering projects and concepts. Often dynamic modeling is used using the platform STELLA. Ecological modeling research also includes environmental accounting, which quantifies the direct and indirect contribution that nature makes to socioeconomic systems, specifically the field of eMergy which incorporates the total amount of energy required to make another form of energy. Emergy is embodied energy that includes environmental contributions (e.g., water, wind) and human services. Our work in ecological modeling includes eMergy, dynamics modeling of digesters and the incorporation of the anaerobic digestion ADM1 model into the STELLA platform.