The aim of this study was to integrally address the uncertainty associated with all the steps used to estimate community drug consumption through the chemical analysis of sewage biomarkers of illicit drugs. Uncertainty has been evaluated for sampling, chemical analysis, stability of drug biomarkers in sewage, back-calculation of drug use (specific case of cocaine), and estimation of population size in a catchment using data collected from a recent Europe-wide investigation and from the available literature. The quality of sampling protocols and analytical measurements has been evaluated by analyzing standardized questionnaires collected from 19 sewage treatments plants (STPs) and the results of an interlaboratory study (ILS), respectively. Extensive reviews of the available literature have been used to evaluate stability of drug biomarkers in sewage and the uncertainty related to back-calculation of cocaine use. Different methods for estimating population size in a catchment have been compared and the variability among the collected data was very high (7–55%). A reasonable strategy to reduce uncertainty was therefore to choose the most reliable estimation case by case. In the other cases, the highest uncertainties are related to the analysis of sewage drug biomarkers (uncertainty as relative standard deviation; RSD: 6–26% from ILS) and to the back-calculation of cocaine use (uncertainty; RSD: 26%). Uncertainty can be kept below 10% in the remaining steps, if specific requirements outlined in this work are considered. For each step, a best practice protocol has been suggested and discussed to reduce and keep to a minimum the uncertainty of the entire procedure and to improve the reliability of the estimates of drug use.