Uncertainty in discharge data must be critically assessed before data can be used in, e. g. water resources estimation or hydrological modelling. In the alluvial Choluteca River in Honduras, the river-bed characteristics change over time as fill, scour and other processes occur in the channel, leading to a non-stationary stage-discharge relationship and difficulties in deriving consistent rating curves. Few studies have investigated the uncertainties related to non-stationarity in the stage-discharge relationship. We calculated discharge and the associated uncertainty with a weighted fuzzy regression of rating curves applied within a moving time window, based on estimated uncertainties in the observed rating data. An 18-year-long dataset with unusually frequent ratings (1268 in total) was the basis of this study. A large temporal variability in the stage-discharge relationship was found especially for low flows. The time-variable rating curve resulted in discharge estimate differences of -60 to +90% for low flows and +/- 20% for medium to high flows when compared to a constant rating curve. The final estimated uncertainty in discharge was substantial and the uncertainty limits varied between -43 to +73% of the best discharge estimate.