The influence of membrane filtration modes on the estimation of size distribution for natural elements in water was investigated. The stepwise membrane filtration is used to distinguish different size fractions including large particulate (>18 μm), particulate (0.2–18 μm), colloidal/nanoparticle (10 kDa–0.2 μm), and truly dissolved fractions (<10 kDa) in river water samples and wastewater treatment plants effluents. Dead-end and tangential flow filtrations were compared during fractionation process. For most elements, concentrations in different size fractions obtained by two filtration modes were generally similar. The obvious difference was only found in acid fractions for some elements, which might be related to the cake grown at membrane surfaces between two filtration modes. In case of elemental partitioning, the influence of filtration modes was normally negligible, when the membranes used and operational factors were exactly the same.