Bedload transport can fluctuate considerably over relatively short periods of time and for a given quasi‐constant flow rate. What are the implications of replacing the fluctuating signal with a smoothed signal when calculating bedload transport using averaged values, as is common practice? This question was investigated with the BedloadR code, which allows 1D bedload calculation as well as Monte Carlo simulations using a new data set collected in the Severaisse River (French Ecrins massif). Four bedload equations (Camenen & Larson, 2005, https://doi.org/10.1016/j.ecss.2004.10.019; Meyer‐Peter & Mueller, 1948; Parker, 1990, https://doi.org/10.1080/00221689009499058; Recking, 2013a, https://doi.org/10.1061/(asce)hy.1943‐7900.0000653) were selected for their performance relative to the measured bedload (except for and Meyer‐Peter and Mueller) and because each equation has a different mathematical form and degree of nonlinearity. They were used in a Monte Carlo approach, with input probability distributions fitted to the measured river width, slope, bed grain‐size distribution, and to the associated (computed) Shields stress. The results show that accounting for natural variability in the calculation reproduces bedload fluctuations well. But overall, when calculating the bedload volume transported by a flow event, accounting for variability systematically leads to higher estimated volumes (of the order of 20%) than those obtained with a deterministic approach using average input parameters. This is a direct consequence of the nonlinearity of the equations.