In recent years, with increased effort to bypass and guide fragile stocks of juvenile salmon in the Columbia Basin past hydroelectric projects, it has been increasingly important to obtain fine-scale fish behavior data in a non-intrusive manner. The Dual-Head Multibeam Sonar is an emerging technology for fisheries applications that addresses that requirement. It has two principal advantages over traditional hydroacoustic techniques: 1) it allows for simultaneous large-volume coverage of a region of interest, and 2) it affords three-dimensional tracking capability. The use of Dual-Head Multibeam Sonar in this study resulted in an unprecedented insight into fine-scale smolt behavior upstream of a prototype surface collector at the Bonneville Dam first powerhouse in 1998. Our results indicated that outmigrant juvenile salmon had an increased likelihood of milling or holding. This discovery will lead to better design criteria for future bypass and collector systems. Future fisheries multibeam sonar systems will likely be fully integrated systems with built-in real-time tracking capability. These systems may be used to track targets relative to physical guidance structures or other behavior-modifying stimuli such as light, turbulent flow, electrical/magnetic fields, or low-frequency sound and vibration. The combination of fine-scale fish behavior data and environmental parameters will yield better design criteria for the safe passage of listed or endangered species of Pacific salmon.