This paper presents a methodological approach that was recently developed to determine alternatives for control of California ground squirrels (Spermophilus beecheyi) and the resulting ecological consequences at the Concord Naval Weapons Station (CNWS). The U.S. Navy initiated this study upon determining a need to control ground squirrels for safety reasons. The squirrel's ecological role at CNWS was examined by estimating squirrel abundance and distribution throughout CNWS, analyzing predator diets, and determining the squirrel's relationship to the California tiger salamander (Ambystoma californiense). In addition, the efficacy of live capture and translocation of squirrels as a possible control method was specifically examined using an experimental approach. Finally, alternative control measures are reviewed and discussed in the context of our results. The emphasis of this paper is on the methods employed and the discussion of alternatives as an example of an ecologically-based approach to control programs. As wide-scale poisoning control programs have recently come under public opposition in the courts and otherwise, studies such as these will serve to direct future management efforts toward control programs that consider several alternatives and their ecological effects.