The threatened Pecos Bluntnose Shiner, Notropis simus pecosensis, is restricted to a 333-km segment of the Pecos River, New Mexico. This is a relatively long, undammed segment, but the flow regime is highly modified and the river channel is degraded. Within the occupied segment, upstream river sections are less-degraded with a wider river channel and shifting-sand substrata, whereas downstream river sections have increasingly narrow river channels and compacted, silt-sand substrata. We studied the longitudinal distribution, length-structure, and population status of N. s. pecosensis from 1992 through 2005. On average, individuals were larger upstream and smaller downstream. Highest densities were in upper-middle portions of the study area. Infrequent high-density collections from lower river sections included only small juveniles that were displaced from upstream. In contrast, high-density collections from upper-middle river sections included all life stages. Thus, we concluded that the core population was restricted to upstream river sections. These river sections have relatively diverse habitat when streamflow is perennial, but are largely desiccated during streamflow intermittence. The core population of N. s. pecosensis was evenly distributed between 1992 and 2000, when streamflow was perennial, but became patchily distributed among refugial habitats between 2001 and 2003, in response to low discharge and periodic streamflow intermittence. High density collections resulted from the concentration of fish in refugia. However, N. s. pecosensis percent species composition declined during this period, indicating that refugia were unsuitable. Low density collections observed after perennial streamflow was restored in 2005 indicated a population collapse between 2001 and 2005. Streamflow intermittence is a threat to the core population of N. s. pecosensis, but habitat degradation appears to limit its distribution. Thus, channel restoration and perennial base-flow will both be important for conservation and recovery.