According to the continued generation of spent nuclear fuel, a reliable safety assessment is highly required with the precise modeling of the migration and retardation behavior of radionuclides to enhance public acceptance and hinder excessive conservativeness during the construction of the repository. In particular, the colloids formed in the repository-relevant condition are known to accelerate the migration of radionuclides. Thus, geochemical behavior and relevant characteristics of colloids are needed to be unambiguously clarified. The objective of the present work is to investigate the fundamental characteristics of colloids contained in the natural groundwater system by using various analytical methods and the tangential flow ultra-filtration (TFUF) system. The granitic groundwater sample from the DB-3 borehole at the KURT (KAERI Underground Research Tunnel) was taken by an airtight stainless steel cylinder coated on the inside with PTFE to prevent the infiltration of ambient air into the geologic groundwater sample. And then, the groundwater sample was transferred to the inert glovebox filled with Ar gas to monitor the pH and Eh equilibrium of the aqueous sample. For further investigation, the colloid contained in the groundwater sample was concentrated by using the TFUF system equipped with a membrane filter (pore size: 3 kDa). The concentrated groundwater sample was analyzed with various methods such as ICP-MS/OES, IC, DLS/ELS, FE-TEM/SEM-EDS, ATR-FTIR, TOC, LC-OCD, etc. In this study, the size of groundwater colloids was determined to be 182.3 ± 52.7 nm with the major constituents of C, S, O, Fe, Al, Si, etc. The amount of organic carbon and the concentrations of organic substances determined by means of the molecular weight fraction with the TOC and LC-OCD provide further detailed information for the colloids in the KURT groundwater sample. The results obtained in this study are expected to be used as preliminary experimental data for modeling the colloid-facilitated migration of radionuclides to improve the reliability of the safety assessment of the geologic repository.