The geothermal characteristics of specific areas on Earth can be identified using geophysical and lithological logs based on deep boreholes, such as those more than 1000 m in depth. Based on the combined analyses of geophysical logs (temperature, caliper, electrical conductivity (EC), and natural gamma-ray logs) and lithological logs, as well as 1D steady-state heat transfer model, the deep groundwater flow and temperature were characterized in four deep boreholes (BH-1–BH-4) roughly 2000 m deep in the area of Heunghae-eup, Pohang, South Korea. The estimated thermal gradients from the temperature profiles are as follows: 22.37–30.77 °C/km for BH-1, 35.67–64.52 °C/km for BH-2, 40.85–46.44 °C/km for BH-3, and 33.33–35.71 °C/km for BH-4. According to the geophysical logs and lithology profiles, the groundwater mainly flows into and out of the boreholes through the basic dyke, rhyolite, and sandstone/mudstone. Evidently, the groundwater flows moving through the fractures and faults induce nonlinear temperature changes. The upward and downward groundwater flows passing through fractures and faults can be estimated using a 1D steady-state heat-transfer equation, by considering a fracture angle based on the lithological and geophysical profiles. To determine the direction (up/down) and rate of groundwater flow, the values for the parameter β were estimated as follows: −1.95 to 5.40 for BH-1, −13.48 to 4.87 for BH-2, −1.76 for BH-3, and −3.39 to 14.15 for BH-4.