Prison substance use is amajor concern for prison authorities and thewider community. Australia has responded to this problemby implementing the National Corrections Drug Strategy. Across Australia, the true extent of prison substance use cannot be determined. As a result, the effectiveness of the interventions employed as part of this strategy cannot be properly assessed. This has important implications for the allocation of corrective services resources and future policy development. This article explores the benefits and limitations, as well as the ethical and practical issues in using wastewater analysis (WWA) to measure levels of substance use in prisons. It reports results fromthe first application ofWWA to an Australian prison, which supports the use ofWWA in this context. Given the increasing concern for prescription misuse in prisons, we also highlight the novel use ofWWA tomeasure the extent of prescription misuse by prisoners. The article concludes that as a result of its objectivity, sensitivityand cost-effectiveness, the use ofWWA in prisons warrants further consideration in Australia.