Driving from advances of two main projects in France (AMPERES and ARMISTIQ), this paper covers the recommendations for sampling and analytical methods for the quantification of priority and emerging micropollutants concentrations and fluxes in wastewaters and sludge, and addresses a new methodology for assessing robust micropollutant removal efficiencies in wastewater treatment plants. The proposed calculation rules take into account the limit of quantification and the analytical and sampling uncertainty of measured concentrations. We identified six cases for which a removal efficiency value is reliable and four other cases where result is highly variable (uncertain) due to very low or unquantified concentrations in effluent or when the influent-effluent concentrations differential is below the measurement uncertainty. The influence of the proposed calculation rules on removal efficiency values was scrutinized using actual results from research projects. The main results obtained in these two projects in terms of micropollutants concentration and removal efficiency are synthetized.