This study employs an integrated groundwater-surface water (GW-SW) model, using SWAT-MODFLOW, to assess groundwater recharge and withdrawals at a regional scale in eastern Nepal. The model components were calibrated and validated using monthly river flow and hydraulic head data for the 1979-2017 period. Our results demonstrate that the average annual groundwater discharge is 2.43 m3/s. Seasonally, the average groundwater discharge is 2.73 m3/s during Summer and is 2.13 m3/s during winter. We observe that the maximum (6.9 m3/s) and minimum (0.036 m3/s) rates occurred in September-October and March-April, respectively. We also find that the average runoff fraction (i.e., runoff/ precipitation) varied from 0.34 to 0.72, and the ET component varied from 0.24 to 0.547 of the total precipitation within the SWAT model. The yearly fluctuation in TWS varied from ± 9.9% to ± 58% of the total precipitation. The Aquifer thickness varies from 16m to 57 m, and the specific yield in the Sunsari district varied from 0.12 lps to 890 lps. In the southern part, we see the water level declines from 2-4 m from July to August, where the bottom water slowly declines in September. The recharge of 1380 l/sec is observed in the Sapta Koshi area in the Bhabar zone. There is substantial underflow from hills simultaneously, resulting in the total recharge in the Sunsari district of 1.98 MCM/yr. At the same time, the total discharge, including surface, sub-surface, and spring water discharge, is nearly 29.2 MCM/yr. This study shows that the Sunsari district’s water resources have many groundwater and surface water, properly managed for future use.