Non-equilibrium molecular dynamics simulations were conducted for solid-liquid-solid systems with nanometer scale grooved surfaces and an induced heat flux for a wide range of topology and solid-liquid interaction conditions to investigate the mechanism of solid-liquid heat transfer, which is the first work of such extensive detail done about the nanoscale roughness effect on heat transfer properties. Single-atom molecules were used for liquid, and the solid-liquid interaction was varied from superhydrophobic to superhydrophilic, while the groove scale was varied from single atom to several nanometers, while keeping the surface area twice that of a flat surface. Both Wenzel and Cassie wetting regimes with a clear transition point were observed due to the capillary effect inside larger grooves that were more than 5 liquid molecule diameters, while such transition was not observed at smaller scales. At the hydrophobic state, large scale grooves had lower interfacial thermal conductance (ITC) due to the Cassie regime, i.e., having unfilled grooves, while at the hydrophilic state, grooved surfaces had ITC about twice that of a flat surface, indicating an extended heat transfer surface effect regardless of the groove scale. At the superhydrophilic state, crystallization of liquid at the surface occurred, and the packing of liquid molecules had a substantial effect on ITC regardless of the groove scale. Finally, both potential energy of solid-liquid interaction and work of solid-liquid adhesion were calculated and were shown to be in similar relations to ITC for all groove scales, except for the smallest single-atom scale grooves, due to a different heat transfer mechanism.