Failures of urban stormwater runoff management can lead to flooding. Potentially toxic elements (PTEs) are commonly found in water runoff and flood. Thus, the population and receiving ecosystems can be exposed to chemical hazards. However, floodwater quality is usually overlooked. In the rainy season, flooding is a persistent problem in the city of Hermosillo, Sonora, Mexico. Thus, the present research deals with the content of PTEs in floodwater, possible threats to receiving ecosystems and flood-affected population. Aluminum (Al), iron (Fe) and zinc (Zn) showed the highest maximum concentrations, which were higher than those observed in runoff in other cities. The PTEs concentrations exceeded Mexican, Australian and the United States guideline criteria. Groups of PTEs sharing similar concentrations were identified relating to their sources and origin: i) stannum (Sn), arsenic (As), chromium (Cr) and silver (Ag); ii) cadmium (Cd), cobalt (Co), antimony (Sb), selenium (Se), beryllium (Be), nickel (Ni), Zinc (Zn), lead (Pb), and thallium (Tl). Potential non-carcinogenic health effects and cancer risk were observed in the floodwater analyzed indicating that management measures should be taken to protect the flood-affected population. The results show that floodwater represents a source of chemical hazards, hence their quality must be monitored to reduce possible related risks.