The influence of wastewater treatment plant (WWTP) effluents from one microelectronic industrial zone on element concentrations and partitioning in river 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 WWTP effluents. Results demonstrated that anthropogenic inputs (WWTP effluents and industrial area) had an important influence on concentrations and partitioning of some elements in river water. Mass balance results showed that membrane filtration processes could realize a good fractionation for many elements (good recoveries) in water samples. Flux decline during 0.2 μm and 10 kDa filtrations were analyzed, and corresponding fouling mechanisms are discussed.