Ever-changing production campaigns complicate the management of recovery and treatment options for unavoidable effluents at pharmaceutical plants. Each campaign produces large amounts of by-products differing in their number, amount as well as composition. Future business strategies designed to address changing market demands add uncertainty to this already challenging design problem. In such a dynamic and uncertain environment, the selection of operating policies as well as decisions to support future business operations by plant investments such as new reactors and separators is a formidable task. This paper will introduce a systematic planning methodology for obtaining long-term waste management strategies for entire batch manufacturing sites. Rigorous modeling of future business and regulatory changes will allow plant managers to assess their long-term monetary, infrastructural and ecological impact. The methodology will be illustrated with the help of quasi industrial case studies. (C) 2003 Elsevier Ltd. All rights reserved.