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.