This work address hyperspectral imaging systems use for maritime target detection using unmanned aerial vehicles. Specifically, by working in the creation of a hyperspectral real-time data processing system pipeline. We develop a boresight calibration method that allows to calibrate the position of the navigation sensor related to the camera imaging sensor, and improve substantially the accuracy of the target geo-reference. We also develop an unsupervised method for segmenting targets (boats) from their dominant background in real-time. We evaluated the performance of our proposed system for target detection in real-time with UAV flight data and present detection results comparing favorably our approach against other state-of- the-art method.