This paper focuses on GNSS-R signal processing techniques applied to water body detection using a low altitude airborne carrier. We develop a radar technique for automatic GNSS signal segmentation in order to differentiate water body surfaces in landforms. In the context of this work, we introduce a mixture of on-line/off-line change detection system that takes into account the radar signal characteristics for segmentation. We propose a new GNSS-R sensor with its implementation on a lightweight airborne carrier. We show, along a real flight experimentation, that the proposed radar technique provides high temporal (50 Hz) and spatial (100 to 300 m2 ) resolution observations of the scanned surfaces. We also show that the proposed automatic segmentation technique can detect in-land water body surfaces.