Safe geological disposal of spent nuclear fuel (SNF) requires knowledge of the deep hydrochemical characteristics of the repository site. Here, we conducted a set of deep hydrochemical investigations using a 750-m borehole drilled in a model granite system in Wonju, South Korea. A closed investigation system consisting of a double-packer, Waterra pump, flow cell, and water-quality measurement unit was used for in situ water quality measurements and subsequent groundwater sampling. We managed the drilling water labeled with a fluorescein dye using a recycling system that reuses the water discharged from the borehole. We selected the test depths based on the dye concentrations, outflow water quality parameters, borehole logging, and visual inspection of the rock cores. The groundwater pumped up to the surface flowed into the flow cell, where the in situ water quality parameters were measured, and it was then collected for further laboratory measurements. Atmospheric contact was minimized during the entire process. Before hydrochemical measurements and sample collection, pumping was performed to purge the remnant drilling water. This study on a model borehole can serve as a reference for the future development of deep hydrochemical investigation procedures and techniques for siting processes of SNF repositories.