Permeability characteristics in coarse-grained soil is pivotal for enhancing the understanding of its seepage behavior and effectively managing it, directly impacting the design, construction, and operational safety of embankment dams. Furthermore, these insights bridge diverse disciplines, including hydrogeology, civil engineering, and environmental science, broadening their application and relevance. In this novel research, we leverage a Convolutional Neural Network (CNN) model to achieve the accurate segmentation of coarse-grained soil CT images, surpassing traditional methods in precision and opening new avenues in soil granulometric analysis. The three-dimensional (3D) models reconstructed from the segmented images attest to the effectiveness of our CNN model, highlighting its potential for automation and precision in soil-particle analysis. Our study uncovers and validates new empirical formulae for the ideal particle size and the discount factor in coarse-grained soils. The robust linear correlation underlying these formulae deepens our understanding of soil granulometric characteristics and predicts their hydraulic behavior under varying gradients. This advancement holds immense value for soil-related engineering and hydraulic applications. Furthermore, our findings underscore the significant influence of granular composition, particularly the concentration of fine particles, on the tortuosity of water-flow paths and the discount factor. The practical implications extend to multiple fields, including water conservancy and geotechnical engineering. Altogether, our research represents a significant step in soil hydrodynamics research, where the CNN model’s application unveils key insights into soil granulometry and hydraulic conductivity, laying a strong foundation for future research and applications.