The North American boreal ecosystem is extensive yet little long-term, ecosystem-level study of it exists. Interest has heightened in recent decades on how this ecosystem will respond to global change. The boreal Wallace Lake watershed (116 ha) on Isle Royale has been under study since 1982. The Lake Superior Basin receives moderate atmospheric hydrogen, nitrogen, and sulfur inputs. In recent decades, regional temperatures have increased and precipitation declined. At Wallace, annual hydrogen and sulfate inputs have declined. The canopy retains precipitation hydrogen and nitrate, but throughfall sulfate flux increases. Relative to canopy throughfall, soil water base cation, bicarbonate, and sulfate flux increase while hydrogen, nitrate, and ammonium decline. Stream water base cation and bicarbonate concentrations have increased due to reduced runoff. Watershed hydrogen and sulfate outputs declined. With snowmelt, stream water acid neutralization capacity declined from dilution. Seasonal changes in stream water ion concentration and flux suggest watershed outputs of nitrogen and sulfate are regulated primarily by soil processes and hydrologic flowpath, functions sensitive to climate change.