The scientific and civilian applications of unmanned aerial vehicles (UAVs) are rapidly expanding. The most common scientific uses are in the fields of archaeology, geography, mining, and civil engineering. Hydrosystem mapping using UAVs is both lean and agile, with the added advantage of increased safety for the surveying crew. However, a common parameter needed in river ecosystem studies is the bulk flow velocity, which cannot be obtained from aerial imagery alone. Recent works have successfully applied large scale particle image velocimetry (LSPIV) using UAVs in rivers, focusing predominantly on surficial flow estimation using differences between images. This work introduces a new methodology for real-time particle tracking in rivers (RAPTOR). This technique performs large scale particle tracking velocimetry (LSPTV) using a combination of floating, infrared light-emitting particles and a programmable embedded color vision sensor in order to simultaneously detect and track the positions of hundreds of objects. The main advantage of this approach is its ability to rapidly collect and process the velocity data, which can be done in real-time. The disadvantage is that the method requires the use of specialized light-emitting particles which in some cases cannot be retrieved from the investigation area. This work introduces the RAPTOR system, data processing workflow, and provides examples of velocity field estimation using the proposed method.