This article examines the way in which the California State Water Resources Control Board (the SWRCB) had dealt with questions relating to scientific uncertainty in making policy for the protection of the Bay-Delta Estuary for the past two decades. Faced with an extensive drought from 1987 to 1992, the SWRCB in 1995 established water quality objectives (California’s term for water quality standards) that would have substantially increased the minimum flows from the Delta into San Francisco Bay, including those required from the San Joaquin River. During the subsequent hearing that addressed which water agencies would be required to provide water to meet the new water quality objectives, the SWRCB agreed to a proposal to engage in a long-term experiment in the face of competing perspectives on how to restore the San Joaquin River component of the Bay-Delta Estuary. In formally adopting this proposal in 2001, the SWRCB adopted something of a hybrid approach to uncertainty. On the one hand, the SWRCB mandated certain flows at certain times of the year, regardless of what was otherwise occurring in the Bay-Delta Estuary. On the other hand, the SWRCB also mandated certain water agencies to release short-duration/large quantity “pulse flows” and required the operators of the federal Central Valley Project (the CVP) and the State Water Project (SWP) to protect fish on a “real-time” basis and curtail project operations to avoid entrainment. Hence, the SWRCB adopted a regulatory regime that generally called for fixed standards but allowed a portion of the regulated community to experiment in a controlled manner that limited the adverse effects on the fishery.