The distinct isotopic composition of metallic elements observed in different sources and reservoirs provides an important perspective on tracing the source, transportation, and circulation of metal pollutants. As an essential trace element for life, Zinc (Zn) will show strong toxicity when its concentration reaches a certain limit. The riverine suspended particulate matter (SPM) is the common occurrence state of Zn. However, few studies have examined the sources and isotope of Zn in SPM. To examine the origins of Zn in SPM, the Zn isotope (δ66Zn) and Zn contents of SPM from 22 sites in the Zhujiang River were investigated and the relative contributions of potential sources to particulate Zn were also calculated. The results indicate that the Zn concentrations have a large variation from 49 to 733 mg kg−1 and a relatively higher enrichment level (EFZn, up to 20.8). The percentage of Zn transportation in the form of SPM ranges between 9% and 97% (average 83%) in the Zhujiang River. The roughly negative correlation is reflected between EFZn and δ66Zn (−0.11‰ to 0.41‰). Based on isotopic mass balance, the contribution of the natural and anthropogenic sources was calculated. The relative proportion of particulate Zn derived from anthropogenic inputs is 30.2%, while the natural source contributes 69.8% Zn to the fluvial SPM. These results further indicate that Zn is controlled by both the natural and anthropogenic inputs. Moreover, the preliminary application of Zn isotope shown in this study highlights the metallic isotope can be an effective indicator of the riverine eco-environmental pollution.