To promote the coordinated development of waterway engineering and ecological protection and advance the high-quality development of inland waterways, this paper systematically reviews the research advances and development directions of ecological impact assessment technology for waterway engineering. It first elaborates on the development history of ecological impact assessment technology, thoroughly explores the impacts of inland waterway engineering on river ecosystems, and depicts the process of constructing an assessment index system that includes the impact on habitat. Meanwhile, various assessment methods such as the time series comparison method, the comprehensive index method, and the analytic hierarchy process are introduced. Finally, development proposals are made such as perfecting the assessment methods and index system, strengthening data collection and monitoring work, and promoting technological innovation and application, with the aim of promoting the high-quality development of China’s inland waterways.