The current study focuses on the understanding of contamination status, distribution, source apportionment and health perspectives of arsenic (As), uranium (U) and other co-occurring trace metals in the groundwater samples collected along the major rivers in Sindh and Punjab provinces, Pakistan. ICP-MS analysis revealed that the concentrations of As in the groundwater in Sindh and Punjab ranged from 0.2 to 81.1 µg/L (n = 38) and 1.1 to 501.1 µg/L (n = 110), respectively. Importantly, this study is the first evidence of U contamination in the groundwater samples in Pakistan, which revealed the concentrations of U at from 0.8 to 59.0 and 0.1 to 556.0 µg/L respectively, in Sindh and Punjab. Moreover, the concentrations of Sr and Mn exceeded the WHO limits in the current study area. Anthropogenic activities such as urbanization, direct dispose of industrial, agricultural waste into waterways and extensive use of pesticides and fertilizers might be the main sources of elevated levels of total dissolved solids and electrical conductivity, which increased the mobilization of As, U and Sr in the groundwater samples. Human health risk assessment parameters such as average daily dose, hazard quotient (HQ) and cancer risk indicated severe risks of As and U in the study area. The HQ values of As and U in Punjab were observed at 69.6 and 7.7, respectively, implying the severity of the health risks associated with consumption of contaminated groundwater for drinking purposes. In a nutshell, proactive control and rehabilitation measures are recommended to eradicate trace metals associated groundwater contamination in the targeted areas to avoid future worst scenarios.