Napier grass is an energy crop that is promising for future power generation. Since Napier grass has never been planted extensively, it is important to understand the impacts of Napier grass plantations on local energetic, environmental, and socioeconomic features. In this study, the soil and water assessment tool (SWAT) model was employed to investigate the impacts of Napier grass plantation on runoff, sediment, and nitrate loads in Songkhla Lake Basin (SLB), southern Thailand. Historical data, collected between 2009 and 2018 from the U-tapao gaging station located in SLB were used to calibrate and validate the model in terms of precipitation, streamflow, and sediment. The simulated precipitation, streamflow, and sediment showed agreement with observed data, with the coefficients of determination being 0.791, 0.900, and 0.997, respectively. Subsequently, the SWAT model was applied to evaluate the impact of land use change from the baseline case to Napier grass plantation cases in abandoned areas with four different nitrogen fertilizer application levels. The results revealed that planting Napier grass decreased the average surface runoff and sediment in the watershed. A multidisciplinary assessment supporting future decision making was conducted using the results obtained from the SWAT model; these showed that Napier grass will provide enhanced benefits to hydrology and water quality when nitrogen fertilizers of 0 and 125 kgN ha−1 were applied. On the other hand, the benefits to the energy supply, farmer’s income, and CO2 reduction were highest when a nitrogen fertilization of 500 kgN ha−1 was applied. Nonetheless, planting Napier grass should be supported since it increases the energy supply and creates jobs while also reducing surface runoff, sediment yield, nitrate load, and CO2 emission.