This study aimed to determine the environmental and health risks of the heavy metal levels in the Danube River in Hungary. The metals, including Fe, Mn, Zn, Cu, Ni, Cr, Pb, and As, were measured in the period from 2013 to 2019. The Spearman correlation and heatmap cluster analysis were utilized to determine the origin of pollution and the factors that control surface water quality. Several indices, such as the heavy metal pollution index (HPI), metal index (MI), hazard quotient oral and dermal (HQ), hazard index oral and dermal (HI), and carcinogenic risk (CR), were conducted to evaluate the potential risks for the environment and human health. The values of the HPI were between the range of 15 < HPI < 30, which indicated moderate pollution; however, the MI results showed high pollution in Dunaföldvár and Hercegszántó cities. The ecological risk (RI < 30) and HI values (< 1) showed low environmental risks and non-carcinogenic impacts of the existing metals, either on adults or children. The mean CR value of oral arsenic was 2.2E−04 and 2.5E−04 during April–September and October–March, respectively, indicating that children were the most vulnerable to arsenic-carcinogenic oral effects. While lead’s CR oral values for children during April–September exceeded the threshold of 1.0E−04, chromium’s oral and dermal CR values for both adults and children were 2.08E−04, 6.11E−04, 1.97E−04, and 5.82E−04 during April–September and October–March, respectively. These results demonstrate the potential carcinogenic risks related to chromium exposure within the two pathways in Hungary and highlight the need for effective measures to mitigate these risks.