Stream water quality and ecological balance can be substantially affected by pH changes. The change in the pH that one would otherwise expect to be induced by the influx of acidic or alkaline wastes can be significantly reduced by the buffering action of indigenous biochemical reactions. Accurate prediction of the magnitude of induced pH change thus requires information on the strength of the natural buffer system and on its resistance to the effects of various wastes. Analysis of system pH response and buffer capacity was approached through an example of anaerobic biological stabilization of waste organic materials. Simulation of the recognized sequential conversion of complex organic materials through acid production and methane fermentation permitted identification of some of the primary processes and provided a basis for the development of an acid-base equilibrium model reflective of buffer capacity during either normal or distressed conditions. The model can be used to predict the effects of organic wastes on natural aquatic ecosystems and thereby provides potentially important input to control the operation of conventional waste treatment processes.