Ecosystem-level experiments are essential in assessing the effects of environmental perturbations like acidification. The Little Rock Lake Acidification Project was initiated to expand insights from previous acidification experiments with whole drainage lakes to a seepage lake system. It involves the gradual acidification of a small (18 ha), seepage lake in northcentral Wisconsin. The goals are to document the biological and chemical changes which occur, to identify the direct and indirect mechanisms which regulate responses, and to expand insights to a class of lakes previously understudied. In the paper, the authors describe the history and rationale of the project and they discuss in general terms the utility and constraints of whole-ecosystem manipulations.