Abstract. To establish the relevance of in-stream processes on nutrient export at catchment scale it is important to accurately estimate whole-reach net nutrient uptake rates that consider both uptake and release processes. Two empirical approaches have been used in the literature to estimate these rates: (a) the mass balance approach, which considers changes in ambient nutrient loads corrected by groundwater inputs between two stream locations separated by a certain distance, and (b) the spiralling approach, which is based on the patterns of longitudinal variation in ambient nutrient concentrations along a reach following the nutrient spiralling concept. In this study, we compared the estimates of in-stream net nutrient uptake rates of nitrate (NO₃) and ammonium (NH₄) and the associated uncertainty obtained with these two approaches at different ambient conditions using a data set of monthly samplings in two contrasting stream reaches during two hydrological years. Overall, the rates calculated with the mass balance approach tended to be higher than those calculated with the spiralling approach only at high ambient nitrogen (N) concentrations. Uncertainty associated with these estimates also differed between both approaches, especially for NH₄ due to the general lack of significant longitudinal patterns in concentration. The advantages and disadvantages of each of the approaches are discussed.