The article proposes a methodology for measuring and processing results, integrating data obtained from Terrestrial Laser Scanning (TLS) with Computational Fluid Dynamics (CFD) analyses, aimed at evaluating water flow conditions in a real-world Small Hydropower Plant (SHP) system. Based on TLS data, a detailed 3D model of the SHP (located in Koszalin, Poland) geometry was developed, which was used to conduct a series of numerical simulations in ANSYS Fluent. The analyses covered six water flow variants, including simulated scenarios accounting for different widths of potential dam leakages. The results confirmed that using TLS data as the basis for the geometric model enables the investigation of actual water flow in the hydropower system. The developed 3D SHP model achieved an accuracy of ±0.02 m relative to the acquired point cloud, and the analyses performed based on it allowed for the evaluation of water flow in the system. The study showed that, in the case of a sealed intake chamber, outlet number 2 handles the largest water mass, accounting for 39.2% of the total flow, while outlets number 1 and 3 account for 33.9% and 26.9%, respectively. The proposed use of TLS data for 3D modeling for water flow analyses in SHP systems highlights the significant potential of integrating TLS and CFD as a widely applicable engineering tool.