Applications of video in fisheries research range from simple biodiversity surveys to 3-dimensional (3-D) measurement of complex swimming, schooling, feeding, and territorial behaviors. However, researchers lack a transparently developed, easy-to-use, general-purpose tool for 3-D video measurement. Thus, we developed a new measurement system, with freely available, user-friendly software, easily obtained hardware, and flexible underlying mathematical methods capable of high precision and accuracy. The software, VidSync, allows users to efficiently record, organize, and navigate complex 2-D or 3-D measurements of fish and their physical habitats. Laboratory tests showed sub-millimeter accuracy in length measurements of 50.8-mm targets at close range, with increasing errors (mostly < 1 %) at longer range and for longer targets. A field test on juvenile Chinook salmon feeding behavior in Alaska streams found that individuals within aggregations avoided the immediate proximity of their competitors, out to a distance of 1.0 to 2.9 body lengths. This system makes 3-D video measurement a practical tool for laboratory and field studies of aquatic or terrestrial animal behavior and ecology.