Evaluating and improving water use efficiency is considered one of the main ways of tackling water shortage challenges in water-scarce cities. A useful indicator for evaluating industrial water use efficiency is the relative water use efficiency (RWUE). In this paper, an industrial RWUE evaluation scheme is proposed based on data envelopment analysis (DEA) theory. In this scheme, the RWUE is divided into overall efficiency (OE), pure technical efficiency (PTE), and scale efficiency (SE). In order to help decision-makers specify the focal industry of efficiency improvement, direct water use is distinguished from indirect water use. By employing this industrial RWUE evaluation scheme, this research calculated the industrial RWUEs for 25 representative industries of Beijing (1990–2010). Results show that the OE, PTE, and SE of Beijing have improved significantly. In the primary industry, the scale adjustment fundamentally lifted OE. For the secondary industries, there still exists much room for water use efficiency improvement in technical innovation. Some emerging tertiary industries replaced traditional tertiary industries as the most efficient water users. This study serves as a valuable reference for the implementation of the Strictest Administration of Water Resources (SAWR) of China, and provides policy-makers worldwide with a useful framework of understating industrial water use efficiency.