Nanotechnology offers a viable solution to enhancing agricultural sustainability by supporting seed germination and crop growth. Besides augmenting crop yields and mitigating the effects of abiotic stresses on crops, nanoparticles (NPs) can also serve as carriers to amplify the effectiveness of fertilizers and pesticides by facilitating their gradual or highly targeted release. However, application of NPs in agricultural systems can result in interaction with crops and pave the way for transfer along the food chain, which raises concerns for consumers. To address these matters, this article provides a comprehensive review of the tracking of various NPs delivered to crops through different uptake pathways. Three types of NPs (including inorganic, carbon-based, and organic NPs) are highlighted for uptake, transport, and their impact on crop growth in agricultural crops. NPs can enter the plant via seeds, roots, and leaves, while the translocation of NPs mainly involves the apoplastic and symplastic pathways. The influence of NPs on plant growth highly depends on the specific plant species as well as the type, size, charge, and concentration of NPs. NPs emit fluorescence through inherent photoluminescence or in combination with fluorescent dyes, which enables monitoring of their distribution within the crop. The benefits and challenges of NPs are discussed, establishing signposts for future research that will enable NPs to contribute to precise and sustainable agriculture.