The uptake, transport, storage, and processing of semivolatile organic chemicals (SVOCs) by vegetation plays an important role in their environmental fate. Understanding these processes at the plant cellular level is essential to understanding the fate and behavior of SVOCs within the environment. Traditional analytical methods have relied on destructive analysis of the plant and a level of inference to suggest exactly where within the plant the chemical is residing, how it is getting there, and what its subsequent fate might be. The use of two-photon excitation microscopy to visualize the in situ uptake, transport, storage, compartmentalization, processing, and fate of a number of polycyclic aromatic hydrocarbons (PAHs) in living vegetation is summarized. Using this technique, the uptake of PAHs to leaves and roots via the atmosphere or soil is visualized. Subsequent storage, transport, compartmentalization, and plant processing, including metabolism, can then be monitored. Differences in processing of the same chemical between species are observed, including compartmentalization, transport routes, and degradation pathways. Chemical location within the plant is observed to have a significant effect on PAH fate (e.g., through photodegradation). We highlight a number of key findings and the research areas requiring increased impetus to gain a comprehensive understanding of the complexity involved in SVOC–plant interactions from the cellular to global scales.