Habitat fragmentation and changes in flow regime can structure fish assemblages, resulting in extirpations or invasions. A guild of freshwater stream fishes that spawn semi-buoyant, nonadhesive eggs directly in the water column are particularly susceptible to extirpation in fragmented streams. The pelagic broadcast-spawning Rio Grande Silvery Minnow Hybognathus amarus was listed as endangered in 1994 and has been intensely managed since. I used mean May flows and the number of times the channel dried within a year to predict numbers of Rio Grande Silvery Minnow captured in isolated pools in the Middle Rio Grande, New Mexico. Adult Rio Grande Silvery Minnow numbers increased as previous year's mean May discharge increased, and generally decreased with each subsequent drying event. Similarly, numbers of young-of-year Rio Grande Silvery Minnow increased with increasing mean May discharge in the current year. However, young-of-year minnow were either very abundant or nearly absent in isolated pools, depending on mean May discharge. Overall trends show a strong decrease in total yearly numbers of adult and young-of-year Rio Grande Silvery Minnow collected in isolated pools from 2009 to 2014, coupled with an increase in the proportion of hatchery-reared adults. Overall numbers fell from >1,000/km in 2009 to <15/km in 2014. Hatchery-reared fish increased from 0% in 2009 collections to 90% in 2014 collections. Managers should focus recovery efforts on providing spring flows that improve recruitment, and avoiding consecutive years of low spring flow because any population recovery will likely be negated by three consecutive years of recruitment failure. A self-sustaining population of Rio Grande Silvery Minnow is unlikely without management options that mitigate the effects of multiyear droughts.