Allylthiourea (ATU) and chlorate (ClO 3 −) are often used to selectively inhibit nitritation and nitratation. In this work we identified challenges with use of these compounds in inhibitory assays with filter material from a biological rapid sand filter for groundwater treatment. Inhibition was investigated in continuous-flow lab-scale columns, packed with filter material from a full-scale filter and supplied with NH 4 + or NO 2 −. ATU concentrations of 0.1–0.5 mM interfered with the indophenol blue method for NH 4 + quantification leading to underestimation of the measured NH 4 + concentration. Interference was stronger at higher ATU levels and resulted in no NH 4 + detection at 0.5 mM ATU. ClO 3 − at typical concentrations for inhibition assays (1–10 mM) inhibited nitratation by less than 6%, while nitritation was instead inhibited by 91% when NH 4 + was supplied. On the other hand, nitratation was inhibited by 67–71% at 10–20 mM ClO 3 − when NO 2 − was supplied, suggesting significant nitratation inhibition at higher NO 2 − concentrations. No chlorite (ClO 2 −) was detected in the effluent, and thus we could not confirm that nitritation inhibition was caused by ClO 3 − reduction to ClO 2 −. In conclusion, ATU and ClO 3 − should be used with caution in inhibition assays, because analytical interference and poor selectivity for the targeted process may affect the experimental outcome and compromise result interpretation. </p