Emerging pollutants (EPs) have become a global concern, attracting tremendous attention because of serious threats to human and animal health. EP diversity emanates from their behaviour and ability to enter the body via multiple pathways and exhibit completely different distribution, transport, and excretion. To better understand the in vivo behaviour of EPs, we reviewed radiolabelling and in vivo radionuclide imaging tracking of various EPs, including micro- and nano-plastics, perfluoroalkyl substances, metal oxides, pharmaceutical and personal care products, and so on. Because this accurate and quantitative imaging approach requires the labelling of radionuclides onto EPs, the main strategies for radiolabelling were reviewed, such as synthesis with radioactive precursors, element exchange, proton beam activation, and modification. Spatial and temporal biodistribution of various EPs was summarised in a heat map, revealing that the absorption, transport, and excretion of EPs are markedly related to their type, size, and pathway into the body. These findings implicate the potential toxicity of diverse EPs in organs and tissues. Finally, we discussed the potential and challenges of radionuclide imaging tracking of EPs, which can be considered in future EPs studies.