Uncertainty in the estimation of hydrologic export of solutes has never been fully evaluated at the scale of a small-watershed ecosystem. We used data from the Gomadansan Experimental Forest, Japan, Hubbard Brook Experimental Forest, USA, and Coweeta Hydrologic Laboratory, USA, to evaluate many sources of uncertainty, including the precision and accuracy of measurements, selection of models, and spatial and temporal variation. Uncertainty in the analysis of stream chemistry samples was generally small but could be large in relative terms for solutes near detection limits, as is common for ammonium and phosphate in forested catchments. Instantaneous flow deviated from the theoretical curve relating height to discharge by up to 10% at Hubbard Brook, but the resulting corrections to the theoretical curve generally amounted to <0.5% of annual flows. Calibrations were limited to low flows; uncertainties at high flows were not evaluated because of the difficulties in performing calibrations during events. However, high flows likely contribute more uncertainty to annual flows because of the greater volume of water that is exported during these events. Uncertainty in catchment area was as much as 5%, based on a comparison of digital elevation maps with ground surveys. Three different interpolation methods are used at the three sites to combine periodic chemistry samples with streamflow to calculate fluxes. The three methods differed by <5% in annual export calculations for calcium, but up to 12% for nitrate exports, when applied to a stream at Hubbard Brook for 1997–2008; nitrate has higher weekly variation at this site. Natural variation was larger than most other sources of uncertainty. Specifically, coefficients of variation across streams or across years, within site, for runoff and weighted annual concentrations of calcium, magnesium, potassium, sodium, sulphate, chloride, and silicate ranged from 5 to 50% and were even higher for nitrate. Uncertainty analysis can be used to guide efforts to improve confidence in estimated stream fluxes and also to optimize design of monitoring programmes.