Bathymetric Laser Scanning (BLS) enables high-resolution mapping of underwater topography using green-wavelength laser pulses that penetrate the water column. However, precise georeferencing of the BLS data is affected by refraction at the air–water interface, which displaces submerged features and affects conventional strip adjustment methods. This paper introduces an integrated refraction-aware georeferencing workflow that combines refraction correction with trajectory and boresight optimization within a unified adjustment framework. Implemented using the scientific OPALS laser scanning software, the workflow starts with direct georeferencing of uncorrected laser returns, derives a water surface model, applies Snell’s law-based refraction correction, and performs iterative strip adjustment until convergence. The approach was validated using UAV-borne topo-bathymetric LiDAR data from Lake Alm (Almsee) in Upper Austria, captured with a <em>RIEGL</em> VQ-840-GE sensor system. Comparative analysis across multiple processing scenarios demonstrates that the proposed integrated method significantly improves internal consistency between overlapping flight strips. The residual height discrepancies, quantified by the median absolute deviation (<em>σ<sub>MAD</sub></em>), were reduced from 4.5 cm using standard processing workflows to 2.1 cm with the integrated approach — an improvement exceeding 50%. A single processing pass was sufficient for the relatively calm conditions of the test site, though iterative refinement may benefit more dynamic water surfaces. The presented methodology is generic and can be embedded in any laser scanning framework supporting modular georeferencing and refraction correction.