To investigate the hydraulic characteristics of fish-friendly culverts, a numerical model of a fish-friendly culvert with triangular lateral baffles was developed based on the large eddy simulation method. Three-dimensional numerical simulation of flow within the culvert was conducted under various submergence levels, and the accuracy and reliability of the numerical model were validated through flume experiments. The results indicate that at half the height of the baffle, flow separation occurs along the outer edge of the baffle, and the size of the recirculation zone increases as the submergence level decreases. The intensity of the shear layer and the turbulence around the baffle are negatively correlated with the submergence level. Under shallow flow conditions, vortex shedding becomes more chaotic, with stronger and more numerous vortex structures near the water surface compared to those near the bed.