This study examines the relationship between Pecos River flow rates and in-stream water depth and velocity. Recent studies of the threatened Pecos Bluntnose Shiner Minnow (PBSM) suggest that water depth and water velocity are key parameters in defining minnow habitat preference. However, river flows that provide sufficient preferred habitat to support this species have yet to be determined. This article discusses available biologic data defining PBSM preferred habitat and develops a predictive model that relates river flows to available depths and velocities across the Pecos River. A novel technique is developed to visualize “habitat-availability curves,” which establish available PBSM habitat as a continuous function of river flow according to whether the water depth is less than 2, 4, 6, 8, 10, 12, or 18 in. (5, 10, 15, 20, 25, 31, or 46 cm) or for threshold velocity values of 0.10, 0.30, 0.50, 0.70, 0.90, 1.1, 1.3, and 1.5 ft/second (3.0, 9.1, 15, 21, 27, 34, 40, and 46 cm/sec). This model is supported and validated with data collected at 11 permanent transects on weekly to monthly bases for more than 1 year. The data and modeling results demonstrate the potential to optimize river flows that present the PBSM with the most habitat using the least flow.