Sediment sources information has considerably enhanced our knowledge of patterns of soil erosion, sediment delivery and deposition in a watershed. It also has great significance for the development of effective sediment and nonpoint source pollution control strategies. Sediment fingerprinting technique has been widely used as a reasonable and reliable means for investigating sediment sources in different watersheds in the world. In recent two decades, rapid progresses have been made in methods improvement, such as fingerprints selection and unmixing model optimization, and also in application range, such as different spatial-temporal scales and different sources classifications. Even more, sediment fingerprinting technique is now transforming from a research tool to a management tool. This paper reviewed the development of fingerprinting technique in aspects of research scales, fingerprints selection, source contribution apportionment and uncertainty analysis. This review also examined the current problems associated with the methodology and identified some research needs for further investigation in the future.