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The shortage of available freshwater is a major global issue worldwide and an increasing demand for clean water requires efficient water purification strategies. Here we describe a method to drastically increase the efficiency of a microreactor for photocatalytic water purification. To find out how the shape of the catalyst affects water purification, nanostructured catalysts of different structures, such as dense film, nanorod, and nanohelix, are prepared and their water purification characteristics are analyzed. Compared to the flat catalyst, the nanostructured catalyst showed a distinct ability in its pollutant degradation, but the detailed structural variation does not significantly affect the water purification. To further increase efficiency, we apply a micromixer to nanorod-based microreactor, which allows even enhanced mass transfer. This enables the solution of the water purification problem and greatly contributes to the industries where the efficiency of photocatalytic activity has attracted extensive interest.