Nutrient addition experiments are commonly used for reach‐scale quantification of in‐stream nitrogen uptake. Traditional, short‐term nutrient addition experiments are subject to nutrient saturation effects, which influence the measured uptake rates, and are not transport based, which limits their ability to distinguish between channel and hyporheic processes. We developed a transport‐based nutrient addition approach adapted to account for the effect of nutrient saturation. We incorporated the Michaelis‐Menten saturation‐limited uptake function into the One‐dimensional Transport with Inflow and Storage (OTIS) solute transport model and specifically designed the field experiments for this modified version of the model (called OTIS‐MM). Cross‐method evaluations were performed for estimates of NH4+ and NO3− uptake lengths (Sw). For NH4+, OTIS‐MM and sequential, multiple‐level traditional experiments produced almost identical Sw values (124 versus 122 m), and the slopes of the regression lines relating Sw to added concentration were similar (4% difference). For NO3−, the methods produced similar Sw values (872 versus 909 m), but the slopes of the regression lines relating Sw to added concentration were different (23% difference). We complemented the cross‐method evaluations with sensitivity analyses for both NH4+ and NO3−, which confirmed that the estimates of the OTIS‐MM uptake parameters were robust. Our field‐modeling approach can easily be designed to cover multiple, sequential reaches in one single addition; hence, it allows for increased spatial coverage.