Abstract: To investigate the heavy metal pollution risk in the water environment of wetlands in arid regions, a total of 36 water samples from representative small water bodies in Urumqi City of northwestern China in October 2023 were collected for analyzing the contents of six heavy metals, including Hg, As, Cu, Zn, Pb, and Cd. The pollution load index (PLI), potential ecological risk index (RI), and ecological risk warning index (I_ER) were used to analyze the pollution levels and ecological risk of heavy metals in the small wetlands in Urumqi city. The results showed that the average Hg contents of the urban and rural small wetlands in the study area were equal to 3.2 and 5.0 times, respectively, of the Class II thresholds of the ‘Environmental Quality Standards for Surface Water’ (GB 3838-2002), whereas the average contents of the other five heavy metals were lower than the corresponding limit values of the Class II thresholds. Results of pollution load index indicated that Hg in the small wetlands in the study area fall into the heavy pollution level, while the other five heavy metals fall into the no-pollution level. The average PLI value of heavy metals in the small wetlands fall into the no-pollution level. The ecological risk assessment results indicated that the Hg in the urban and rural small wetlands in the study area fall into the strong, very strong ecological risk level, respectively, whereas the other five heavy metals fall into the low ecological risk level. The average RI value of heavy metals in the urban and rural small wetlands fall into the low, moderate ecological risk level, respectively. Hg in the urban and rural small wetlands in the study area fall into the light, moderate risk warning level, while other five heavy metals fall into the no-warning risk level. The average I_ER value of heavy metals in the urban and rural small wetlands fall into the no-warning level. Overall, the contents, pollution levels, and potential ecological risk of heavy metals in the rural small wetlands were higher than those of the urban small wetlands in the study area. Hg is the main pollution factor and ecological risk factor in the small wetlands. This is related to the high Hg level in soil as well as human activities in Urumqi city. Obtained results of this study can provide a theoretical basis for the ecological security protection of small wetlands in Urumqi city.