Dams have fragmented habitat and altered the natural river hydrograph. Sumner Dam blocks the transport of sediment into occupied habitat and has created unsuitable habitat from the dam down to the confluence with Taiban Creek. The flow regime in the Pecos River is highly modified and is dictated by water irrigation needs. No attempt has been made to mimic the natural hydrograph. Spring runoff from headwater streams is captured in Santa Rosa Reservoir and is released in blocks to maximize transport efficiency. Although the block releases in some aspects mimic a natural flood (rapid increase in discharge), the high discharge lasts much longer (7–14 days compared to 1–2 days), and is of much less magnitude than pre-dam flood events. Although the Pecos Bluntnose Shiner uses block releases for spawning, because of the extended time of high flow and the loss of riparian habitat complexity leading to diminished egg retention, a portion of their eggs and larvae (estimates range from 8–60%) is flushed downstream during extended high flow releases and lost in Brantley Lake. Because the block releases are always of the same magnitude (1,400 cfs or 42 m3/s), the channel has adjusted to this flood magnitude, causing the channel to become narrower, less braided, and to have less diverse fish habitat. In upper critical habitat, undammed tributaries occasionally create floods greater than the block releases and add sediment to the river. For these reasons upper critical habitat maintains more of a natural character and suitable habitat for all life stages. Lower critical habitat consistently has water but the habitat quality is poor. Because of the poor habitat quality and proximity to Brantley Reservoir, it is questionable whether lower critical habitat could maintain a population without input of individuals from the upper reach. Source: USFWS (2010).
The biggest threat is river intermittency. The negative effect of intermittency on the population has been documented. Although the Bureau of Reclamation is committed to keeping the river whole between Sumner Dam and Brantley Reservoir, its options for maintaining flow are currently limited. If climate change leads to drier and/or hotter conditions, it is unlikely that intermittency could be prevented with the water currently available for Pecos Bluntnose Shiner conservation. Source: USFWS (2010).
Although golden algae are not currently a threat to Pecos Bluntnose Shiner, with climate change (decreases in flow, greater proportion of flow coming from agricultural return, leading to increased nutrient and salt concentrations) golden algae could become an issue in portions of the river, depending on how the river is managed. Because of unsuitable habitat below Brantley Reservoir and repeated fish kills from golden algae, expansion of the range downstream is not feasible. Loss of Pecos Bluntnose Shiner, as well as three of four of the other native pelagic spawners, between Santa Rosa and Sumner Dams, indicates that either the habitat is unsuitable or the reach of river is not long enough to sustain this pelagic spawning fish (i.e., loss of reproductive effort to Sumner Reservoir exceeds that needed to sustain a population). Pelagic spawning fish have been extirpated from nearly all short (less than 100 km) river reaches in the Rio Grande basin. The reach between Santa Rosa Dam and Sumner Reservoir is approximately 100 km, but only about 40 km is potentially suitable habitat. Thus, successful expansion of the population above Sumner Dam is unlikely. Source: USFWS (2010).
The reach of the Pecos River between designated critical habitat zones is of high quality when it remains wetted, and the Pecos Bluntnose Shiner can attain high densities in this area. Based on population monitoring before, during, and after river intermittency, USFWS (2010) concluded that maintaining water in this reach is important for sustaining the population as a whole and is an important element for the Pecos Bluntnose Shiner's recovery.
It is anticipated that climate change will add to the difficulty in maintaining flow throughout occupied habitat. An extended or intense drought will exceed the ability of managers to keep the river whole, given current operations and the amount of water available for Pecos Bluntnose Shiner conservation. During periods of drought, as was seen in 2002 and 2003, Fort Sumner Irrigation District's water right exceeds the amount of water in the river. The challenge of the coming decades will be finding sufficient water to maintain the species and satisfy agricultural demand. Source: USFWS (2010).