The ILWAS model was used as a framework to evaluate processes regulating the acid base chemistry of diverse lake types in the Adirondack Mountain region of New York State. The lakes selected for study represented both drainage and seepage basins distributed across regional edaphic and climatic gradients. Seventeen of the sites constitute a system of drainage lakes within the North Branch of the Moose River, located in the west-central Adirondacks. Variability in watershed characteristics of sub-basins in this drainage system and a wide range in surface water chemistry (pH 4.2–7.4) facilitated analysis of primary processes regulating surface water acidification. Additionally, the effects of these watershed acidity gradients on fish species distribution was assessed from recent and historical fish collections and by in situ bioassay to evaluate relative species sensitivity to acidity. Considerable variation in processes controlling acid-base chemistry of Adirondack lakes, both within drainage systems and regionally, were found as a result of variability in soil characteristics (primarily soil depth and mineralogy). hydrologic flowpaths, and reduction processes (both in-lake and watershed) controlling sulfate and nitrate concentrations. Soil characteristics and hydrologic flow paths largely determined base cation supply rates, whereas both hydrology and reduction processes effectively regulated acid anions supplied principally from atmospheric deposition. Inter-watershed acidity gradients related to these controlling processes and interspecific variation in physiological acid tolerance were found to be important determinants of fish species distribution patterns. Fish species with low acid tolerance (particularly cyprinids) had either disappeared from acidified lakes and streams or were found only in areas exhibiting low acidity. Currently, acid tolerant fish species (e.g., Yellow Perch,Percaflavescens) inadvertently introduced into Adirondack waters predominate in acidified drainage systems.