The variability of climate, increase in population, and lack of territorial plans in Costa Rica have caused intense disasters with human and economic losses. In 2016, Hurricane Otto hit the country’s northern area, leaving substantial damages, including landslides, debris flows, and flooding. The present study evaluated different scenarios to estimate flooded areas for Newtonian (clean water), and non-Newtonian flows with volumetric sediment concentrations (Cv) of 0.3, 0.45, 0.55, and 0.65 using Hydro-Estimator (HE), rain gauge station, and the 100-year return period event. HEC–HMS modeled the rainfall products, and FLO-2D modeled the hydrographs and Cv combinations. The simulation results were evaluated with continuous statistics, contingency table, Nash Sutcliffe Efficiency, measure of fit (F), and mean absolute differences (E) in the floodplains. Flow depths, velocities, and hazard intensities were obtained in the floodplain. The debris flood was validated with field data and classified with a Cv of 0.45, presenting lower MAE and RMSE. Results indicated no significant differences in flood depths between hydrological scenarios with clean-water simulations with a difference of 8.38% in the peak flow. The flood plain generated with HE rainfall and clear-water condition presented similar results compared to the rain gauge input source. Additionally, hydraulic results with HE and Cv of 0.45 presented E and F values similar to the simulation of Cv of 0.3, demonstrating that the HE bias did not influence the determination of the floodplain depth and extent. A mean bias factor can be applied to a sub-daily temporal resolution to enhance HE rain rate quantifications and floodplain determination.