No quarter: Lack of refuge during flow intermittency results in catastrophic mortality of an imperiled minnow

Many once-perennial rivers have become intermittent. Channel drying can result in fish mortality if refuges are not available. Understanding where refuges occur and if fishes use these refuges can provide insight for species persistence and help stakeholders manage limited resources. Streamflow diversions in the Rio Grande of New Mexico can result in >60 km losses of aquatic habitat, affecting up to 30% of the range of imperiled Rio Grande silvery minnow (Hybognathus amarus). Potential refuges include areas with perennial flow below diversion dams, isolated pools, and irrigation return flows. We examined spatial and temporal patterns of both adult and young-of-year Rio Grande silvery minnow collected in isolated pools that formed during streamflow intermittency from 2009 to 2019. We hypothesised that: (1) Rio Grande silvery minnow would be more numerous in pools that persisted longer; (2) they would be more numerous in isolated pools located closer to upstream areas of perennial flow, due to upstream movement to escape drying; and (3) increased rate of aquatic habitat loss each day would result in more Rio Grande silvery minnow in isolated pools. During the 12 years of the study, we counted Rio Grande silvery minnow in 3,985 isolated pools that formed during streamflow intermittency. We related counts of Rio Grande silvery minnow in each pool to the maximum pool depth, rate of loss of aquatic habitat that occurred that day, and distance each pool was to an upstream barrier. In 2016, we examined persistence of 290 isolated pools until complete desiccation or reconnection with continuous flows occurred, and the factors that influenced pool persistence. Deeper pools persisted for longer, but depth had a small positive effect on counts of adult Rio Grande silvery minnow and no effect on counts of young-of-year in isolated pools. Adults were more numerous in upstream isolated pools, whereas young-of-year were more numerous in downstream isolated pools. Rate of channel drying had little effect on the numbers of adult Rio Grande silvery minnow in isolated pools, but more young-of-year were stranded when the rate of drying was faster. On average, pools persisted <4 days and 263 of 290 dried completely before continuous flows returned. Only 66 of 4,749 Rio Grande silvery minnow occurred in pools that did not dry completely. Rio Grande silvery minnow did not appear to escape channel intermittency; instead, they became stranded in shrinking isolated pools that did not persist long enough to act as refuges for fishes. Lack of refuge during channel intermittency would result in catastrophic mortality of fishes through complete desiccation of pools if there were no management actions, such as translocating fish. To increase persistence through streamflow intermittency, conservation actions should match the species response to intermittency by ensuring the availability of perennial-water refuges at the appropriate spatial and temporal scale.