Deterministic simulations using the SWAN model were conducted along a stretch of the Tietê-Paraná waterway in the Ilha Solteira dam reservoir, São Paulo, Brazil, to assess the water waves generated by winds. Simultaneously employs a probabilistic metamodeling approach (PCE) and Sobol indices, to quantify uncertainty of the five involved physical parameters (wind velocity and direction, bottom friction (JONSWAP), whitecapping and depth-induced breaking index). In the deterministic part, Janssen’s formulation yielded the most successful and accurate estimations of wave heights. Probabilistic analysis underscored the importance of wind data and the whitecapping parameter in model calibration, with a significant influence of wind speed indicated by Sobol indices. The results not only refined the model calibration process, but also allowed the creation of contour maps for wave height and period that offer practical pre-project applications. This work advances understanding of wind wave hydrodynamics deterministically and probabilistically, with good concordance and performance indices compared to field data, despite being scarce.