This study conducts a thermo-economic assessment for hydrogen production utilizing geothermal energy over a 30-year period, with a focus on the often-overlooked heat losses in wells and their impact on system performance. The geothermal system is accurately simulated using a detailed full 3D geometry finite element model that incorporates impervious ground and aquifer layers. A hybrid numerical modelling approach is used, integrating both underground and aboveground components to compare the performance of simple and advanced Organic Rankine Cycle systems against traditional aquifer only models, commonly used for underground components. The findings reveal that the temperature difference between the bottom and top of the production well, caused by heat losses, can have a substantial effect on hydrogen production costs and rates. During the first five years, this temperature difference averages 7.3 °C, resulting in a 28 % variation in hydrogen production rate and a 10.2 % difference in costs. Over the last 10 years, the temperature difference gradually decreased to 1.4 °C, leading to a 6 % variation in hydrogen rate and a 5 % cost difference compared to models that do not account for this well temperature variation. This study demonstrates that including all ground layers in the modelling of hydrogen production systems is critical. The heat exchange between wellbores and the impervious ground mass above the aquifer significantly influences the system's performance, underscoring the need for comprehensive modelling approaches.