The growing use of composite honeycomb structures in several industries including aircraft has demonstrated the need to develop effective and efficient non-destructive evaluation methods. In recent years, active thermography has attracted great interest as a reliable technology for non-destructive testing and evaluation of composite materials due to its advantages of non-contact, non-destructive, full-area coverage, high speed, qualitative, and quantitative testing. However, non-uniform heating, low spatial resolution, and ambient environmental noise make the detection and characterization of defects challenging. Therefore, in this study, lock-in thermography (LIT) was used to detect water ingress into an aircraft composite honeycomb sandwich structure, and the phase signals were binarized through the Otsu algorithm. A square composite honeycomb with dimensions of 210 mm × 210 mm along with 16 different defective areas of various sizes in groups filled with water by 25%, 50%, 75%, and 100% of the cell volume was considered. The sample was excited at multiple modulation frequencies (i.e., 1 Hz to 0.01 Hz). The results were compared in terms of phase contrast and CNR according to the modulation frequency. In addition, the detectability was analyzed by comparing the number of pixels of water ingress in the binarized image and the theoretical calculation.