Abstract The transport of radionuclides by organic colloids in deep groundwater is one of the important issues for the geological disposal of high-level radioactive waste. Because of their low concentration, it is difficult to directly analyze organic colloids in deep groundwater. Hence, it is useful to utilize porous membranes for the condensation which can increase the concentration of organic colloids in groundwater physically without alteration of their properties, although some part of the components is lost by membrane fouling. In this study, hydrodynamic conditions were optimized, and surfaces of nanofiltration (NF) membranes were modified using a cationic phosphorylcholine polymer, poly(2-methacryloyloxyethyl phosphorylcholine-co-2-aminoethyl methacrylate) (p(MPC-co-AEMA)), for preventing membrane fouling and improving condensation efficiency. Aqueous solutions of humic acid or bovine serum albumin (BSA) were used as models of organic colloids, and they were condensed using a laboratory-scale cross-flow filtration apparatus equipped with a commercial sulfonated polyethersulfone NF membrane. The effects of hydrodynamic conditions, such as the applied transmembrane pressure (TMP) and stirring rate, and membrane surface modification on condensation efficiency were evaluated. A low TMP and high stirring rate effectively improved the recovery yield of humic acids and BSA. The membrane surface coated with p(MPC-co-AEMA) was significantly effective for preventing the decline in permeate flux, caused by fouling with BSA. Deep groundwater, obtained from a depth of 300 m at the Mizunami Underground Research Laboratory in Japan, was condensed. The recovery yield of the organic colloids in the deep groundwater condensation test at 5-fold condensation was improved from 62% to 92% by the optimized hydrodynamic conditions and membrane surface modification for prevention of membrane fouling. The composition of organic colloids in the condensates was analyzed using pyrolysis gas chromatography coupled with mass spectrometry.