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Spatial and temporal variability in surface water chemistry, organic soil chemistry and hydrologic indicators were investigated at three poor-fen complexes in two boreal catchments in Northern Alberta to provide insight into the dominant controls on surface water chemistry. Improved understanding of these controls is required to enable prediction of runoff chemistry in the region under changing atmospheric deposition conditions. Surface water chemistry exhibited considerable variability; within each fen conductivity, dissolved organic carbon (DOC), and Cl⁻ tended to decrease and pH tended to increase with increasing distance from the lake edge. Variations in evaporative isotopic enrichment in ²H and ¹⁸O, expressed as deuterium excess, were used to distinguish between throughflow waters and those that were more evaporatively enriched. Throughflow surface waters were more acidic primarily due to higher concentrations of DOC and NO₃ ⁻. Exchangeable base saturation and pH of organic soils were strongly related to surface water chemistry at two of the fen complexes, demonstrating the capacity for cation exchange to influence surface water chemistry. Fen surface water concentrations of most elements and DOC increased during the summer period (between June and August), while pH of water decreased. Evaporative concentration of the surface waters was a dominant driver, with surface water temperature increasing at both catchments. Localized groundwater discharge was an important contributor of base cations to the fens, while the organic soils are sinks for atmospherically deposited SO₄ ²⁻, N and Cl⁻. Copyright © 2010 John Wiley & Sons, Ltd.