The well-known Manning formula is usually used for the calculation of the volumetric flow rate (discharge) in open channels. The discharge depends on the geometry of the channel, i.e. the cross-sectional area, the wetted perimeter and the slope, as well as on the roughness coefficients. All these quantities are determined with some uncertainty. The article proposes a methodology for calculating the uncertainty of the roughness coefficients of the riverbed and the floodplain as well as the uncertainty of the geometric dimensions of the riverbed. Then, the method of calculating the uncertainty of the discharge is then given. If these uncertainties are taken into consideration in the process of discharge calculation, then, as has been demonstrated for a hypothetical river channel, the ratio of the uncertainty to the calculated value of the discharge will change from several dozen percent in case of small flows to about ten percent in case of big, flood flows. It has also been shown that the uncertainty of the roughness coefficients has the biggest influence on the uncertainty of the flow rate. The presented calculations show that in order to take into account the influence of uncertainty of linear dimensions and roughness coefficients, the engineer designing the riverbed should assume for the calculations the flow rate increased by 10% then design flow. The obtained results can be used for homogeneous flows only, which is usually assumed in practical engineering calculations.