Sediment fingerprinting is a technique critical to researches on sources and dynamics of sediment in recent years. However, the technique does have certain limitations, for instance, its multiple assumptions often differ from practical conditions, thus bringing about a series of uncertainties. The process of sediment transportation from source to sink is subject to the interference of natural environment and anthropic activities, so potential variations of source characteristics, migration path, and properties of sediment are all factors of uncertainty in fingerprinting procedure. Moreover, sampling designing, fingerprint selection method, and use of mixing models are subjective factors that further expand sources of uncertainty. Uncertainty analysis is a significant component of the sediment fingerprinting technique, and it is also an important basis for assessing reliability of fingerprinting to identify sources of sediment. This paper reviewed the series of issues of uncertainty in sediment fingerprinting, and progresses in researches addressing these problems and described status quo of the research on quantitative assessment of the uncertainties in an attempt to provide certain recommendations for further investigation.