Due to seasonal differences in production demands, effluent streams from batch manufacturing sites may exhibit considerable variations in number, amount as well as composition. Pharmaceutical and fine chemical production distinguishes itself also in recycling practices since stringent purity requirement often prohibit direct reuse of raw materials in the next batch. Further complications stem from ever changing production campaigns, where each may last only for a few months. In such a dynamic environment, selection of recovery and treatment options as well as assessments of their benefits and tests constitutes a formidable task. Designing plant-wide waste management policies assuming perfect information may not be satisfactory given the variability of the production campaigns. Therefore, this article addresses the problem of finding optimal waste management policies for entire manufacturing sites in the presence of uncertainty. It will offer a mathematical programming framework for implementing three contrasting strategies, Small ease studies exemplify the impact of different perspectives on the structural design decisions in the overall plant design.