Transit time‐based water quality models using StorAge Selection (SAS) functions are crucial for nitrate (NO3−) management. However, relying solely on instream NO3− concentration for model calibration can result in poor parameter identifiability. This is due to the interaction, or correlation, between transport parameters, such as SAS function parameters, and denitrification rate, which challenges accurate parameters identification and description of catchment‐scale hydrological processes. To tackle this issue, we conducted three Monte‐Carlo experiments for a German mesoscale catchment by calibrating a SAS‐based model with daily instream NO3− concentrations (Experiment 1), monthly instream stable water isotopes (e.g. δ18O) (Experiment 2) and both datasets (Experiment 3). Our findings revealed comparable ranges of SAS transport parameters and median water transit times (TT50) across the experiments. This suggests that, despite their distinct reactive or conservative nature, and sampling strategies, the NO3− and δ18O time series offer similar information for calibration. However, the absolute values of transport parameters and TT50 time series, as well as the degree of parameter interaction differed. Experiment 1 showed greater interaction between certain transport parameters and denitrification rate, leading to greater equifinality. Conversely, Experiment 3 yielded reduced parameters interaction, which enhanced transport parameters identifiability and decreased uncertainty in TT50 time series. Hence, even a modest effort to incorporate only monthly δ18O values in model calibration for highly frequent NO3−, improved the description of hydrological transport. This study showcased the value of combining NO3− and δ18O model results to improve transport parameter identifiability and model robustness, which ultimately enhances NO3− management strategies.