Characterisation of the reaction steps involved in nitrification can help determine the processes that produce potentially harmful environmental pollutants such as nitrite, nitrate and nitrous oxide (N2O). The use of nitrification inhibitors can uncouple the reactions and therefore assist in their mechanistic and isotopic characterisation. However, nitrification inhibitors can interfere with the methods for determining the concentrations and stable isotope ratios of ammonium, nitrite and nitrate. The interference of allylthiourca, hydrazine or sodium chlorate in colorimetric methods and stable isotope measurements were assessed. Ammonium concentrations were measured with the salicylate method. Nitrite and nitrate were measured with the Griess reaction, with nitrate first being reduced to nitrite with vanadium (III) chloride. For the stable isotope analysis, nitrite was reduced to N2O in a 1 : 1 sodium azide and acetic acid buffer solution; preceded, when necessary, by ammonium oxidation to nitrite by hypobromite or nitrate reduction to nitrite on an activated cadmium column. Sodium chlorate did not interfere with any of the analyses and none of the inhibitors interfered with the stable isotope ratios determination of nitrate. Allylthiourea interfered with ammonium and nitrate quantification. Both allylthiourea and hydrazine also clearly interfered in the determination of the nitrogen stable isotope ratio of ammonium, while only allylthiourea interfered in the determination of nitrogen and oxygen stable isotope ratios of nitrite. Although we suggest methods to overcome some of these interferences, our study demonstrated that the analytical methods used in combination with allylthiourea or hydrazine as nitrification inhibitors should be considered with caution when designing experiments.