From previous reports, uptake and accumulation of organic compounds by plant roots are strongly related to water solubility. However, the relation between uptake pathways and water solubility remains unclear. Here, we used confocal laser scanning microscopy to observe the uptake of fluorescent hydrophilic and hydrophobic compounds in the living roots of Cucurbita pepo. We found strong regulation of the uptake of berberine, a hydrophobic compound at the endodermal Casparian strip, as previously reported, and similar regulation was also observed in the pericycle. Berberine was loaded into and transported upward through the protoxylem. Perylene, a highly hydrophobic compound, in contrast, passed through the Casparian strip and accumulated preferentially in the endodermis and pericycle. The results of our solvent extraction suggested that perylene diffused into the non-aqueous phase. Therefore, the uptake pathways for the hydrophilic and hydrophobic compoundss are different. These results offer a new way to understand the uptake of agrochemicals and pollutants and to select host plants for phytoremediation.