Structural defects such as separation between concrete slab and foundation, and structural voids often occur in hydraulic engineering, which threatens the safety of hydraulic engineering. As the size and internal material of the hydraulic engineering can be queried, ground penetration radar (GPR) detection has the advantage to detect these defects when compared with other nondestructive detection methods. At the same time, when GPR detection is applied to defect these structural defects in hydraulic engineering, complex environmental factors including the uneven structural surface, clutter interference, water reflection, etc. have to be taken into account. In this work, two experimental models are designed to represent two different types of hydraulic structures and the structural defects including separation between concrete slab and its bottom material and void or hole defects are simulated on the two test models, respectively. Through the GPR detection on the two experimental models, the effects of the three environmental factors on the radar images and the signatures of the radar images under the influence of the three environmental factors are studied. Then, different image processing methods are adopted to reduce the influence of the three different environmental factors, and the effects of these methods are verified using the radar images obtained from the experiments. Finally, the GPR detection on a practical hydraulic engineering influenced by the environmental factors and the image processing methods are investigated, which successfully verify the experimental investigation results. It is expected that this study would provide significant technology support for structural defects detection in hydraulic engineering.