Stocking hatchery-reared fish is a common method used to rebuild endangered species populations that are extirpated or extremely small. However, the success of stocking is often poor and studies are typically needed to evaluate the success of the stocking and refine stocking protocols. The San Juan River Recovery Implementation Program initiated stocking of young Colorado pikeminnow (Ptychocheilus lucius) in the San Juan River of New Mexico in 2002. BIO-WEST was contracted to evaluate survival and retention, growth, and habitat use of Colorado pikeminnow in the San Juan River. BIO-WEST sampled seasonally to evaluate stocking success, and potentially provide information to improve success of future stocking. In 2003 BIO-WEST began experimenting with different acclimation and stocking protocols to examine their impact on retention of stocked Colorado pikeminnow. Most recently, BIO-WEST investigated habitat availability and use by young Colorado pikeminnow. These efforts were the first to quantify this habitat relationship, and they have important implications for the management and conservation of Colorado pikeminnow.