The impact on environment and on health of different pollutants, especially chemical pollutants, is becoming critical due to their drastic consequences on our main vital resource: water. In recent years, extensive efforts of fundamental research and developing practical processes have been devoted to the polluted water treatment. The semiconductor based photocatalytic process has shown a great potential as an environmental friendly and sustainable treatment technology due to its low-cost, and its ability to decompose the wide spectrum of contaminants in wastewater at room temperature without residual deposits that may require further post-treatment. With high surface/volume ratio, the nanostructured semiconductor shows enhanced photocatalytic efficiency in advancing water and wastewater treatment. Among the photocatalytic materials, ZnO nanostructure is a promising candidate for their easy-controllable synthesis, chemical and thermal stability. On the other hand, its further integration in a microfluidic system can overcome the main limitation of low speed mass transfer during the photo-degradation process of polluted water due to the shorter diffusion length within confined micro-chambers. Here we show a high efficiency microfluidic system decorated inside by ZnO nanostructures leading to a high throughput micro-reactor for water purification.