San Acacia Dam is located in a reach of the Rio Grande that has been designated as critical habitat for two endangered species, the Rio Grande silvery minnow (Hybognathus amarus) and the southwestern willow flycatcher (Empidonax traillii extimus). Under present operations, the Rio Grande upstream from the dam is used to convey irrigation water to the Socorro main canal at San Acacia Dam. In order to increase operational flexibility and improve irrigation delivery efficiency, the 'Bernardo Siphon' has been proposed to intercept up to 150 cubic feet per second from the Lower San Juan Riverside Drain on the east side of the Rio Grande and transport it under the river into a drainage canal on the west side. Irrigation deliveries to the Socorro main canal would be conveyed by way of the drainage canal rather than the Rio Grande. The objective of this study was to provide the Bureau of Reclamation (BOR) and other stakeholders with a tool to evaluate the effects of different operational modes of the Bernardo siphon on habitat for H. amarus and E. t. extimus in this section of river. We used a two-dimensional hydraulic simulation model to simulate hydraulic conditions for a range of discharges at three study sites in the Rio Grande between the proposed siphon location and San Acacia Dam. Suitable habitat characteristics were defined for H. amarus by consensus of a panel of experts and for E. t. extimus on the basis of a study conducted in 2003 by BOR. Habitat suitability maps for each targeted life stage and simulated discharge were constructed using a Geographic Information System (ArcGIS) and the results compiled into tables relating discharge to areas of suitable habitat. A separate analysis was conducted to calculate an index of connectivity among habitat patches at low flows. A hydrologic model was constructed to synthesize flows, by reach, without the siphon, which was used as a baseline for comparison with similarly-synthesized discharges with the siphon under different operating rules. Results from the hydrologic time series were combined with the discharge-habitat relations to develop habitat time series models, statistics, and scoring metrics for comparisons of alternative rules of operation for the Bernardo siphon. Suitable habitat for H. amarus was defined as areas having suitable hydraulic conditions alone and as areas having suitable hydraulics in association with large woody debris. Suitable hydraulic habitat for adults was maximized at discharges between 40 and 80 cubic feet per second, and declined rapidly at discharges larger than 150 cubic feet per second. When large woody debris was included in the definition of suitable habitat, discharges between 40 and 200 cubic feet per second provided maximum suitable habitat for adults. Juvenile hydraulic habitat was maximized at discharges between 20 and 80 cubic feet per second, and hydraulic habitat associated with large woody debris was largest at flows between 40 and 150 cubic feet per second. Nesting habitat area for E. t. extimus increased monotonically at discharges larger than 5 ft3/s, but decreased rapidly below that flow.