The interactions between nanomaterials and plants have attracted increasing attention. However, the systemic stress and recovery patterns of plants in response to nanomaterials and the connections between the molecular responses and the phenotypes remain unclear. Herein, rice was exposed to graphene oxide (GO) nanosheets at 0.01-1.0 mg/L for 7 days under hydroponic exposure, followed by a 7-day post exposure (GO-free). The significant upregulation (p < 0.05) of phenylalanine metabolism, secondary metabolism, and heme peroxidase reflected the stress and recovery patterns of rice roots exposed to GO. GO triggered 27% and more than 50% decreases in hydraulic conductivity and aquaporin gene expression (PIP1-3 and PIP2-2), respectively. The uptake of GO was mediated by aquaporin inhibition. Nanomaterial biotransformation reflected the potential for rice roots to adapt to GO stress. Oxidative stress, especially the downregulation of class III peroxidase mRNAs, were suppressed by GO. Lateral root inhibition, primary root growth, and cell wall synthesis, as forms of resistance to GO stress, were related to the significant (p < 0.05) downregulation of salicylic acid and lignin biosynthesis, as well as the upregulation of jasmonic acid and laccases. The present study helps elucidate the molecular and phenotypic responses of plants to nanomaterials, which are closely linked to their environmental risk assessment.