Membrane filtration is one of the main methods of local water treatment. Track-etched membranes allow to obtain high-quality purified water due to their high selectivity. During the filtration, the productivity of process can decreases due to the adsorption of components in the pores, pore blockages, formation of sediment layer above the membrane. To restore the productivity, the membrane should be flushed periodically or regenerated chemically. Comparative study of the back-flushing and chemical regeneration after natural water filtration using standard 12-μm-thick track-etched membrane and new 20-μm-thick irradiated on both sides (with argon ions with the mileage less than the film thickness) was performed. The research was conducted with natural water from the pond "Zenit" (St. Petersburg) and the Volhov River (Leningrad region). The filtration was conducted in the dead-end mode. Water samples were analyzed by spectrophotometry, spectroturbidimetry and dynamic light scattering. The size distribution of impurity particles of studied natural water, the change in their sizes during coagulation with an aqua-aurate were determined in work. The mechanisms underlying the decrease of filtration productivity were identified. The experimental data showed that both-sided irradiated 20-μm-thick membrane has advantages over a standard 12-μm-thick membrane in natural water filtration with impurities that block the pores both in the direct filtration process and in back-flushing and regeneration. The possibility of regeneration and back-flushing of the 20-μm-thick membrane allows us to recommend it for natural water filtration.