The Hsinchu Science Park was established in Taiwan in the 1980s, replacing traditional industries with high value-added and technology-intensive industries. Taiwan has become one of the Newly-Industrialized Economies (NIEs). However, the continued expansion of high-tech enterprises in science parks requires large amounts of resources to be consumed, deteriorating the quality of the environment, for which society must pay a high cost. In this study, the input-output model was used to explore the water footprints of the Hsinchu Science Park. The study results revealed that among the six industries at the Hsinchu Science Park, the integrated circuit industry (whether in 2001, 2004, or 2006) had the lowest total water consumption per unit of output. From a water footprint perspective, compared with the other industries of the science park, the development of the integrated circuit industry has had a lower impact on the environment. Furthermore, the integrated circuit industry, precision machinery industry, and biotechnology industry have become increasingly dependent on foreign water resources to alleviate the water shortage in Taiwan. In contrast to previous studies on water consumption, this study incorporated indirect water usage into the analysis; thus, a comprehensive view of the water consumption of each industry was analyzed from a broad perspective.