The national mandate to protect endangered species requires a scientific understanding of what a species requires to exist. This knowledge is almost always based on insufficient data and often evolves under conditions of continuing experimentation. The protection of aquatic species has led to dramatic confrontations between irrigators and environmentalists. Scientific uncertainty is often at the center of these confrontations, as scientists are asked to provide knowledge that is used to make water management decisions. Science has become the contested arena, leaving scientists bruised by their treatment in the legal and policy arena. This paper will consider the relationship of law and science in the protection of endangered species and ask how it can be improved.