Here we describe a portable stereo camera system that integrates a GPS receiver, an attitude sensor, and 3D stereo photogrammetry to rapidly estimate the position of multiple animals in space and time. We demonstrate the performance of the system during a field test by simultaneously tracking the individual positions of 6 long-finned pilot whales, Globicephala melas. In shore-based accuracy trials, a system with a 50 cm stereo baseline had an average range estimation error of 0.09 m at a 5 m distance increasing up to 3.2 m at 50 m. The system is especially useful in field situations where it is necessary to follow groups of animals traveling over relatively long distances and time periods while obtaining individual positions with high spatial and temporal resolution (up to 8Hz). These positions provide quantitative estimates of a variety of key parameters and indicators for behavioural studies such as inter-animal distances, group dispersion, speed and heading. This system can additionally be integrated with other techniques such as archival tags, photo-identification methods or acoustic playback experiments to facilitate fieldwork investigating topics ranging from natural social behaviour to how animals respond to anthropogenic disturbance. By grounding observations in quantitative metrics the system can characterize fine-scale behaviour or detect changes as a result of disturbance that might otherwise be difficult to observe.