Setting instream flows to protect aquatic resources is required by California state law, but this task is not straightforward for an intermittent river that is naturally dry six or more months of every year. The Santa Maria River, 200 km northwest of the Los Angeles metropolitan area, lies within the northern range of the federally endangered southern California steelhead (Oncorhynchus mykiss) and is a logical candidate for instream flow protection: the watershed historically supported the anadromous life history of this species, but fish must navigate the lowermost 39 km of the commonly dry mainstem river to move between the ocean and freshwater habitats in the upper watershed. Mainstem flows are partly controlled by Twitchell Dam, constructed across one of the Santa Maria River's two main tributaries in 1962. The dam is operated to maximize groundwater recharge through the bed of the mainstem Santa Maria River, thus minimizing discharge to the Pacific Ocean and so reducing already limited steelhead passage opportunities. Conventional criteria for determining suitable instream flows for steelhead passage are ill-suited to intermittent, Mediterranean-type rivers because they ignore the dynamic channel morphology and critical importance of headwater flows in providing cues that once presaged passage-adequate mainstem discharges but no longer do so. Hydrologic analysis of pre-dam flows, coupled with established criteria for successful O. mykiss migration, provides an objective basis for evaluating alternative dam-management scenarios for enhancing steelhead passage, although their implementation would redirect some water that for the past half-century has exclusively supported irrigated agriculture and municipal water supplies. Copyright © 2013 John Wiley & Sons, Ltd.