Ground-source heat pump systems are renewable and highly efficient HVAC systems that utilise the ground to exchange heat via ground heat exchangers (GHEs). This study developed a detailed 3D finite element model for horizontal GHEs by using COMSOL Multiphysics and validated it against a fully instrumented system under the loading conditions of rural industries in NSW, Australia. First, the yearly performance evaluation of the horizontal straight GHEs showed an adequate initial design under the unique loads. This study then evaluated the effects of variable trench separations, GHE configurations, and effective thermal conductivity. Different trench separations that varied between 1.2 and 3.5 m were selected and analysed while considering three different horizontal loop configurations, i.e., the horizontal straight, slinky, and dense slinky loop configurations. These configurations had the same length of pipe in one trench, and the first two had the same trench length as well. The results revealed that when the trench separation became smaller, there was a minor increasing trend (0.5 °C) in the carrier fluid temperature. As for the configuration, the dense slinky loop showed an average that was 1.5 °C lower than those of the horizontal straight and slinky loop (which were about the same). This indicates that, when land is limited, compromises on the trench separation should be made first in lieu of changes in the loop configuration. Lastly, the results showed that although the effective thermal conductivity had an impact on the carrier fluid temperature, this impact was much lower compared to that for the GHE configurations and trench separations.