• Impacts of natural convecton on CBHE’s thermal efficiency is studied. • Various cases of CBHE depth, inflow rate and aquifers permeability are considered. • Inflow rate has a more significant effect on thermal yield when permeability is high. • Shorter CBHE's thermal performance shows more sensitivity to aquifers permeability. Deep borehole heat exchangers (BHEs) can be utilised effectively for geothermal (heat) extraction from up to a few kilometres below the subsurface using the conventional closed U-loop or coaxial configurations. These systems take advantage of the high enthalpy energy in the deeper ground without relying on fracture flow extraction/injection, hence avoiding the complexity and uncertainty of hydraulic fracturing to enhance the permeability of deep aquifers. Despite the recent theoretical advancement in deep BHE systems, recent studies mainly assume conductive heat transfer in the ground, neglecting the effects of groundwater and heat convection (natural or forced) on the system’s thermal capacity. This simplified assumption could result in underestimating geothermal extraction efficiency given the extensive fluctuations in groundwater thermo-physical properties, particularly at high temperatures. Therefore, the ultimate goal of this study is to investigate the extent to which the thermal performance of deep coaxial borehole heat exchangers (CBHEs) is affected by natural convection in deep aquifers. This is achieved by developing a novel numerical approach for reliable quantification of thermal yield, accounting for conduction and the commonly overlooked thermo-induced convection in aquifers - using a tested 3D finite element heat and mass transport model. Considering groundwater parameters’ temperature dependency, the resultant buoyancy in groundwater and the effects of gravity, parametric studies are undertaken for various ranges of permeability, carrier fluid velocity and CBHEs depth. The overall validity of the model is tested against published experimental data. It is concluded that higher carrier fluid inflow rates for a given CBHE depth can lead to up to 43% higher CBHEs thermal efficiency when the aquifer’s permeability is high (k = 10 −10 m 2 ). Furthermore, the results indicate that a higher aquifer permeability, hence a substantial thermo-induced heat exchange in the aquifer, has a more pronounced effect on CBHEs thermal yield than carrier fluid inflow rate in shorter CBHEs (63% vs 17% increase), which contradicts the behaviour of longer CBHEs in which the thermo-induced convective heat transfer in aquifers with higher permeability, i.e., k = 10 −10 m 2 and carrier fluid inflow rate could have a similar effect on the system’s efficiency (45% vs 43% increase). In general, it is concluded that an accurate evaluation of how system parameters such as the inflow rate and CBHE’s depth could contribute to CBHE’s thermal yield requires a good understanding of the impacts of aquifer’s characteristics, i.e., temperatures, permeability and depth on thermo-induced heat exchange in the aquifer, which is facilitated using the proposed numerical model.