The effects of changes in acid deposition rates resulting from the Clean Air Act Amendments of 1990 should first appear in stream waters during rainstorms and snowmelt, when the surface of the watershed is most hydrologically connected to the stream. Early detection of improved stream water quality is possible if trends at high flow could be separately determined. Trends in concentrations of sulfate (SO42−), nitrate (NO3−), calcium plus magnesium (Ca2++Mg2+), and acid-neutralizing capacity (ANC) in Biscuit Brook, Catskill Mountains, New York, were assessed through segmented regression analysis (SRA). The method uses annual concentration-to-discharge relations to predict concentrations for specific discharges, then compares those annual values to determine trends at specific discharge levels. Median-flow trends using SRA were comparable to those predicted by the seasonal Kendall tau test and a multiple regression residual analysis. All of these methods show that stream water SO42− concentrations have decreased significantly since 1983; Ca2++Mg2+ concentrations have decreased at a steady but slower rate than SO42−; and ANC shows no trend. The new SRA method, however, reveals trends that differ at specified flow levels. ANC has increased, and NO3− concentrations have decreased at high flows, but neither has changed as significantly at low flows. The general downward trend in SO42− flattened at median flow and reversed at high flow between 1997 and 2002. The reversal of the high-flow SO42− trend is consistent with increases in SO42− concentrations in both precipitation and soil solutions at Biscuit Brook. Separate calculation of high-flow trends provides resource managers with an early detection system for assessing changes in water quality resulting from changes in acidic deposition.