Streamflow time series are commonly derived from stage‐discharge rating curves, but the uncertainty of the rating curve and resulting streamflow series are poorly understood. While different methods to quantify uncertainty in the stage‐discharge relationship exist, there is limited understanding of how uncertainty estimates differ between methods due to different assumptions and methodological choices. We compared uncertainty estimates and stage‐discharge rating curves from seven methods at three river locations of varying hydraulic complexity. Comparison of the estimated uncertainties revealed a wide range of estimates, particularly for high and low flows. At the simplest site on the Isère River (France), full width 95% uncertainties for the different methods ranged from 3 to 17% for median flows. In contrast, uncertainties were much higher and ranged from 41 to 200% for high flows in an extrapolated section of the rating curve at the Mahurangi River (New Zealand) and 28 to 101% for low flows at the Taf River (United Kingdom), where the hydraulic control is unstable at low flows. Differences between methods result from differences in the sources of uncertainty considered, differences in the handling of the time‐varying nature of rating curves, differences in the extent of hydraulic knowledge assumed, and differences in assumptions when extrapolating rating curves above or below the observed gaugings. Ultimately, the selection of an uncertainty method requires a match between user requirements and the assumptions made by the uncertainty method. Given the significant differences in uncertainty estimates between methods, we suggest that a clear statement of uncertainty assumptions be presented alongside streamflow uncertainty estimates.