Beijing, capital of China, and its exuberant waterfront is supposed to be a significant component of the city’s charm. However, due to urbanization and population growth, Beijing’s waterfront is experiencing a variety of issues, needing comprehensive urban design and overall value assessment. The main purposes of this study are to develop an urban layer system of waterfront urban design and to assess the current and expected value of Beijing’s waterfront. Beijing’s waterfront was divided into four urban layer subsystems: ecological subsystem, spatial subsystem, demand subsystem, and cultural subsystem. This study includes the waterfront of 26 rivers and 9 lakes, which are divided into 54 waterfront segments by main roads. This study assessed the current and expected values of 54 waterfront segments in Beijing with the urban layer system by citizen questionnaires, expert questionnaires, and field surveys. A series of maps and radar maps were generated to visualize the assessment results. This study analyzes and describes the characteristics of four urban layer subsystems and different waterfront segments, based on a comprehensive evaluation of the value of Beijing’s waterfront. It provides strategies for the master urban design of Beijing’s waterfront. Furthermore, the results of this study and the urban layer system can provide insight on waterfront urban design.