Colloids were separated by submicro-filtration of granitic groundwater samples collected at-line under in-situ thermodynamic conditions after down-hole groundwater sampling and transfer at the well head. The methodology avoids the generation of artefacts produced by pH changes due to CO2 exchange, yielding potential carbonate precipitation, or by O2 contamination yielding oxidized insoluble phases. The enhanced pressure and the anoxic conditions are also maintained through the filtering procedure. This procedure was carried out after a period of regular sampling of groundwater pumped to the ground surface and continuous on-line long-term measurements (weeks, months) of chemical and physical parameters in the unbroken sample water both at the ground surface and at depth down-hole. Colloid samples were characterized on the submicro-filtration membrane by scanning electron microscopy. Under deep granite groundwater conditions, natural colloids occur sparsely. The colloid concentration was determined C col ∼1 and ∼50 μg L−1 for sizes ranging from 50 to 200 nm or n col ∼ 3.9 × 109 and 47 × 109 L−1 for sizes larger than 50 nm for KFM11A, Forsmark, and KLX17A, Laxemar, Oskarshamn, respectively, Sweden. These colloids are expected to be clay particles with an average size smaller than 200 nm for the Na-Ca-Cl and Na-Cl groundwaters (pH 7.6 and 8.00, ionic strength ∼10−1 and ∼10−2 mol L−1, respectively, for KFM11A and KLX17A), the colloid concentrations were comparable with values previously reported in the literature.