Long term growth and well being of the chemical industry requires economically and ecologically conscious process engineering. Traditional process engineering methods fall short of meeting this need due to their treating the environment as being secondary to economic objectives. Life cycle assessment and design methods broaden the scope of traditional methods, but focus primarily on the environmental impact of emissions while ignoring the contribution of ecological products and services. Taking nature for granted could provide misleading results since natural products and processes are a significant contributor to all industrial products and processes. Methods from systems ecology do account for ecological inputs, but ignore the impact of emissions. This paper presents an original approach for the joint analysis of industrial and ecological systems. This approach considers inputs from both ecological and economic resources, as well as the impact of emissions. It uses thermodynamics to exploit the synergy between methods from process systems engineering, systems ecology, and life cycle assessment to overcome the shortcomings of methods from each field. The approach is based on the fact that growth and sustenance of both industrial and ecological processes are limited by the available energy and its conversion to useful work. Thus, the embodied energy (emergy), that is, the energy used directly or indirectly to make a product or service is a thermodynamic measure of ecological investment or cost, while exergy loss provides a holistic measure of the impact of emissions. Together, emergy and exergy analysis can provide insight into the environmental performance and sustainability of the industrial process or product. The proposed framework is broadly applicable to assist decision making in chemical and other engineering tasks, Challenges and research opportunities for making this framework practical are identified.