Palaeoflood reconstructions based on stage evidence are typically conducted in data-poor field settings. Few opportunities exist to calibrate the hydraulic models used to estimate discharge from this evidence. Consequently, an important hydraulic model parameter, the roughness coefficient (e.g. Manning's n), is typically estimated by a range of approximate techniques, such as ‘visual estimation’ and semi-empirical equations. These techniques contribute uncertainty to resulting discharge estimates, especially where the study reach exhibits sensitivity in the discharge–Manning's n relation. We study this uncertainty within a hydraulic model for a large flood of known discharge on the Mae Chaem River, northern Thailand. Comparison of the ‘calibrated’ Manning's n with that obtained from semi-empirical equations indicates that these underestimate roughness. Substantial roughness elements in the extra-channel zone, inundated during large events, contribute significant additional sources of flow resistance that are captured neither by the semi-empirical equations, nor by existing models predicting stage–roughness variations. This bedrock channel exhibits a complex discharge–Manning's n relation, and reliable estimates of the former are dependent upon realistic assignment of the latter. Our study demonstrates that a large recent flood can provide a valuable opportunity to constrain this parameter, and this is illustrated when we model a palaeoflood event in the same reach, and subsequently examine the magnitude–return period consequences of discharge uncertainty within a flood frequency analysis, which contributes its own source of uncertainty. Copyright © 2005 John Wiley & Sons, Ltd.