The aim of this study was to examine the relationship between the anisotropy direction of exposed gravel bed and flow direction. Previous studies have shown that the anisotropy direction of a gravel bed surface can be visually determined in the elliptical contours of 2-D variogram surface (2DVS). In this letter, airborne laser scanning (ALS) point clouds were acquired at a gravel bed, and the whole data set was divided into a series of 6 m × 6 m subsets. To estimate the direction of anisotropy, we proposed an ellipse-fitting-based automatic procedure with consideration given to the grain size characteristic d50 to estimate the primary axis of anisotropy [hereafter referred to as the primary continuity direction (PCD)] in the 2DVS. The ALS-derived PCDs were compared to the flow directions (for both high and low flow) derived from hydrodynamic model simulation. Comparison of ALS-derived PCDs and simulated flow directions suggested that ALS-derived PCDs could be used to infer flow direction at different flow rates. Furthermore, we found that the ALS-derived PCDs estimated from any elliptical contour of the 2DVS exhibited a similar orientation when the contours of the 2DVS reveal the clear anisotropic structure, demonstrating the robustness of the technique.