Etheostoma moorei (Yellowcheek Darter), a candidate species for federal listing, is endemic and obligate to headwater riffles of the upper Little Red River drainage in north central Arkansas. Downstream segments of these tributaries were inundated in 1964 as a result of filling of Greers Ferry Reservoir. We compared riffle densities during drought (1999–2001) and non-drought periods (2003–2004), and to historic data (1979–1980). Upstream sites dried periodically during the drought of 1999–2001, and Yellowcheek Darters occupying those sites were extirpated; even at downstream sites, densities were significantly lower than historical levels. During normal precipitation levels during 2003–2004, densities increased significantly, yet several upstream sites and one complete stream remained extirpated. The loss of downstream refugia as a result of the construction of Greers Ferry Dam in 1964 may exacerbate natural climatic cycles, which include drought, resulting in stream-wide extirpations.