PnET-BGC is an integrated biogeochemical model formulated to simulate the response of soil and surface waters in northern forest ecosystems to changes in atmospheric deposition and land disturbances. In this study, the model was applied to five intensive study sites in the Adirondack and Catskill regions of New York. Four were in the Adirondacks: Constable Pond, an acid-sensitive watershed; Arbutus Pond, a relatively insensitive watershed; West Pond, an acid-sensitive watershed with extensive wetland coverage; and Willy's Pond, an acid-sensitive watershed with a mature forest. The fifth was Catskills: Biscuit Brook, an acid-sensitive watershed. Results indicated model-simulated surface water chemistry generally agreed with the measured data at all five sites. Model-simulated internal fluxes of major elements at the Arbutus watershed compared well with previously published measured values. In addition, based on the simulated fluxes, element and acid neutralizing capacity (ANC) budgets were developed for each site. Sulphur budgets at each site indicated little retention of inputs of sulphur. The sites also showed considerable variability in retention of NO3-. Land-disturbance history and in-lake processes were found to be important in regulating the output of NO3- via surface waters. Deposition inputs of base cations were generally similar at these sites. Various rates of base cation outputs reflected differences in rates of base cation supply at these sites. Atmospheric deposition was found to be the largest source of acidity, and cation exchange, mineral weathering and in-lake processes served as sources of ANC. ?? 2004 John Wiley and Sons, Ltd.