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Abstract: Abstract Recent advances in the developments of optical atomic clocks have enabled 10−18-level frequency comparisons between fibre-linked clocks. Therefore, chronometric leveling with an uncertainty on the order of 1 cm has become possible, based on the general theory of relativity. Since measurement uncertainty does not deteriorate with increasing fibre length, applications of chronometric leveling in geodesy, particularly unification of height reference systems, have been actively studied. In Japan, a frequency comparison is under experimentation using a fibre link connecting two optical lattice clocks approximately 100 km apart. This study estimates both the potential difference between these two clock sites with a geodetic method and its uncertainty to verify the results of chronometric leveling, which will be obtained in the near future. We use orthometric heights derived from leveling surveys repeated for monitoring crustal deformation. When discussing an uncertainty at the 1-cm level in height, the effects of temporal variations in the gravitational potential on the height measurement need to be considered due to various geophysical phenomena, including tides. Our results show that the uncertainty in the height measurements by geodetic leveling is the largest and that tidal potential changes during the height measurements can cause systematic errors of a few mm. The effects due to variations in the nontidal ocean bottom pressure and atmospheric pressure are more than an order of magnitude smaller than the tidal effects at this spatial scale. An upper limit of groundwater effects is also estimated. In a future comparison with clocks with an uncertainty on the order of 10−19, tidal potential changes and groundwater effects must be more rigorously evaluated.