Heavy metal(loid) (HM) contamination is a significant threat to wetland ecosystem. However, contamination risks of HMs in overlying water of small wetlands, which are easily ignored because of their minor occupancy in an overall area, are nearly unknown. A total of 36 water samples containing six HMs were collected from the urban and rural small wetlands of Urumqi in China, and the contamination levels and probabilistic health risks caused by HMs were assessed using the Nemerow pollution index (NPI) and the health risk assessment model introduced by the US EPA. The results revealed that the average concentration of Hg in the urban and rural small wetlands surpassed the Class II thresholds of the Environmental Quality Standards for Surface Water (GB 3838-2002) by factors of 3.2 and 5.0 times, respectively. The overall contamination levels of HMs in the small wetlands fall into the high contamination level. Results of a health risk assessment indicated that non-carcinogenic health risk of the investigated HMs are found to be lower than the acceptable range for adults, but higher than the acceptable range for children. Meanwhile, As falls into the low carcinogenic risk level, whereas Cd falls into the very low carcinogenic risk level. Overall, HMs in rural small wetlands showed relatively higher contamination levels and probabilistic health risks than that of urban small wetlands. In addition, As was identified as the dominant health risk factor in the overlying water of small wetlands in the study area. Findings of this study provide scientific support needed for the prevention of HM contamination of small wetlands in arid zones.