Pollution has become a serious issue in the urban water environment as stormwater runoff transports a range of pollutants to receiving water bodies, undermining water quality and posing human and ecosystem health risks. Commonly, the primary focus of stormwater quality research is on the role of pollutants directly accumulating at the ground phase. However, atmospheric phase can also exert a significant impact on stormwater quality through atmospheric deposition. Unfortunately, only limited research has focused on the linkage between atmospheric and ground phases in relation to urban stormwater quality. The study discussed in this paper characterised the four primary transport pathways, atmospheric build-up (AB), atmospheric deposition (AD) and road surface build-up (BU) and wash-off (WO) in relation to heavy metals, which is a key urban stormwater pollutant. The research outcomes confirmed the direct linkage between atmospheric phase and ground phase and in turn the significance of atmospheric heavy metals as a contributing source to stormwater runoff pollution. Zn was the most dominant heavy metal in all four pathways. For the AB pathway, atmospheric heavy metal pollution on weekdays is more serious than weekends. For the AD pathway, dry atmospheric deposition of heavy metals is positively correlated to dry days, whilst wet (bulk) deposition is related to rainfall depth. For the BU pathway, heavy-duty vehicle traffic volume was found to be the most important source. For the WO pathway, industrial and commercial areas tend to produce higher heavy metal concentrations in stormwater runoff than residential areas. The study results will contribute to the creation of effective urban stormwater pollution mitigation strategies and thereby enhancing the quality of the urban water environment.