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This work presents a case study of a wastewater treatment plant (WWTP), located in Biscay (Spain), in which the removal of high-occurrence contaminants of emerging concern (CEC) was studied. The existing biological treatment in the WWTP was complemented with a continuous ultrafiltration (c-UF) pilot plant, as a tertiary treatment. Thus, the effect on CEC removal of both treatments could be analyzed globally and after each operation. A total of 39 CEC were monitored, including pharmaceutical products, industrial additives, food additives, herbicides and personal care products. For evaluation of the efficiencies, the removal rates of the biological and of the c-UF treatments, including their variability over a day and a week in relation to the ammonium content, were examined in the influent of the WWTP. In the biological treatment, a wide range of different removal rates was obtained due to the different CEC’s biodegradability and concentration. In UF, lower, but more constant removal rates, were achieved. In addition, the reduction of the general toxicity by the UF treatment in terms of the Microtox® toxicity assay was also evaluated. After UF, all of the samples yielded values of TU50 lower than 1, confirming this result the UF effectiveness for toxicity removal.