The production of geothermal energy relies on subsurface properties. In low-enthalpy geothermal regimes, thermal energy extracted with a borehole heat exchanger (BHE) is the subsurface heat conducted from the rock and grout to the BHE fluid. Estonian geology provides a good opportunity to investigate how groundwater flow impacts BHE heat production. The hundreds of metres thick sedimentary rock sequence holds four main aquifers. We modelled single BHEs with lengths of 400 m, 500 m and 1000 m and a BHE field of ten 400-m wells at three sites across Estonia. Then, we parametrized different hydraulic conditions to compare how the groundwater flow velocity impacts the thermal energy yield of the systems.Our results indicate that if groundwater flow increases above 0.03 m/day, it increases the total energy yield from 3 % to 20 %. Thermogeological parameters, such as subsurface temperature and thermal conductivity, affect the thermal energy yield of the wells more than the modelled groundwater flow. Our study provides an estimate of the thermal energy yield from different BHE types and the detailed sensitivity analysis. We conclude that geothermal energy is a significant renewable energy resource for Estonia and areas with similar geology and climate.