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The application of an ISO standard procedure (Guide to the Expression of Uncertainty in Measurement (GUM)) is here discussed to quantify uncertainty in human risk estimation under chronic exposure to hazardous chemical compounds. The procedure was previously applied to a simple model; in this article a much more complex model is used, i.e., multiple compound and multiple exposure pathways. Risk was evaluated using the usual methodologies: the deterministic reasonable maximum exposure (RME) and the statistical Monte Carlo method. In both cases, the procedures to evaluate uncertainty on risk values are detailed. Uncertainties were evaluated by different methodologies to account for the peculiarity of information about the single variable. The GUM procedure enables the ranking of variables by their contribution to uncertainty; it provides a criterion for choosing variables for deeper analysis. The obtained results show that the application of GUM procedure is easy and straightforward to quantify uncertainty and variability of risk estimation. Health risk estimation is based on literature data on a water table contaminated by three volatile organic compounds. Daily intake was considered by either ingestion of water or inhalation during showering. The results indicate one of the substances as the main contaminant, and give a criterion to identify the key component on which the treatment selection may be performed and the treatment process may be designed in order to reduce risk.