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Ecosystems constantly adjust to altered biogeochemical inputs, changes in vegetation and climate, and previous physical disturbances. Such disturbances create overlapping ‘biogeochemical legacies’ affecting modern nutrient mass balances. To understand how ‘legacies’ affected watershed‐ecosystem (WEC) biogeochemistry during five decades of studies within the Hubbard Brook Experimental Forest (HBEF), we extended biogeochemical trends and hydrologic fluxes back to 1900 to provide an historical framework for our long‐term studies. This reconstruction showed acid rain peaking at HBEF in the late 1960s‐early 1970s near the beginning of the Hubbard Brook Ecosystem Study (HBES). The long‐term, parabolic arc in acid inputs to HBEF generated a corresponding arc in the ionic strength of stream water, with acid inputs generating increased losses of H⁺and soil base cations between 1963 and 1969 and then decreased losses after 1970. Nitrate release after disturbance is coupled with previous N‐deposition and storage, biological uptake, and hydrology. Sulfur was stored in soils from decades of acid deposition but is now nearly depleted. Total exports of base cations from the soil exchange pool represent one of the largest disturbances to forest and associated aquatic ecosystems at the HBEF since the Pleistocene glaciation. Because precipitation inputs of base cations currently are extremely small, such losses can only be replaced through the slow process of mineral weathering. Thus, the chemistry of stream water is extremely dilute and likely to become even more dilute than pre‐Industrial Revolution estimates. The importance of calculating chemical fluxes is clearly demonstrated in reconstruction of acid rain impacts during the pre‐measurement period. The aggregate impact of acid rain on WEC exports is far larger than historical forest harvest effects, and even larger than the most severe deforestation experiment (Watershed 2) at HBEF. A century of acid rain had a calcium stripping impact equivalent totwoW2 experiments involving complete deforestation and herbicide applications.

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. © 2014 The Authors.Hydrological Processespublished John Wiley & Sons, Ltd.