Sea level rise (SLR) can negatively affect the hydrology of coastal watersheds. However, the relevant information is incomplete and insufficient in existing literature. The objective of this study is to present a modeling approach to predict long-term effects of SLR on changes of flood peak, flood stage, and groundwater table with an assumption that the historical climate would reoccur in the future. The study was conducted for a typical coastal watershed in southeast USA. The results indicate that sea level had been rising at a rate of 4.21 mm yr−1 from 1948 to 1982 but at a faster rate of 5.16 mm yr−1 from 1983 to 2013. At such SLR rates and by 2113, the groundwater table beneath the eastern part of the watershed would be raised by 0.10 to 0.29 m, while the annual mean peak discharge and flood stage at the watershed outlet would be increased by 13.84 m3 s−1 (from 3.63 to 17.47 m3 s−1) and 0.92 m (from zero to 0.92 m), respectively. The other parts of the watershed would be relatively less affected by SLR. For coastal watersheds, SLR will probably raise the groundwater table, and increase the magnitude and occurrence of peak discharge and flood stage.