Livestock production is a major source of pharmaceutical emissions to the environment. The current scientific discourse focuses on measuring and modeling emissions as well as assessing their risks. Although several studies corroborate the severity of pharmaceutical pollution resulting from livestock farming, differences in pollution between livestock types and production systems are largely unknown. In fact, there is no comprehensive analysis of factors influencing pharmaceutical use—the emission's source—in the diverse production systems. To address these knowledge gaps, we developed a framework to investigate pharmaceutical pollution from different livestock production systems and applied it in a first pilot assessment to compare pollution from organic and conventional cattle, pig, and chicken production systems on selected indicator substances, covering antibiotics, antiparasitics, hormones, and nonsteroidal anti‐inflammatory drugs (NSAIDs). Given the lack of statistics, for this article we retrieved novel qualitative information about influential factors for pharmaceutical use and pollution from expert interviews and combined this with quantitative data on, among other factors, the environmental behavior of specific substances from the literature. Our analysis reveals that factors across a pharmaceutical's entire life cycle influence pollution. However, not all factors are livestock type or production‐system dependent. The pilot assessment furthermore reveals that differences in pollution potential between conventional and organic production exist, but for antibiotics, NSAIDs, and partially for antiparasitics, some factors lead to greater pollution potential in conventional systems, and others in organic systems. For hormones, we identified a comparatively greater pollution potential from conventional systems. Among the indicator substances, the assessment over the entire pharmaceutical life cycle illustrates that flubendazole in broiler production has the greatest per unit impact. The framework and its application in the pilot assessment generated insights useful to identifying which substances, livestock types, production systems, or the combination thereof have great or little pollution potential, informing more sustainable agricultural management practices. Integr Environ Assess Manag 2023;00:1–15. © 2023 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).