The rapid increase in the production and application of various types of nanomaterials increases the possibility of their presence in total environment, which subsequently raises concerns about their potential threats to the first trophic level of organisms, specifically under varying environmental constraints. In this work, seeds of Cucurbita pepo L. were cultured in MS basal medium exposed to multi-walled carbon nanotubes (MWCNTs) at different concentrations (0, 125, 250, 500 and 1000 μg mL−1) under two levels of water potential, well-watered (0 MPa) and water stress (−1.5 MPa) induced by polyethylene glycol (PEG 6000) for 14 days. Seeds exposed to MWCNTs showed reduction in germination percentage, root and shoot length, biomass accumulation and vigor index in a dose-dependent manner. However, seedlings germinated in MWCNTs-fortified media had significantly lower germination and growth attributes than those of control under water stress conditions. This happened due to increased oxidative injury indices including hydrogen peroxide (H2O2), and malondialdehyde (MDA) contents, as well as electrolyte leakage index (ELI) of tissues. The impaired morpho-physiological and biochemical processes of seedlings exposed to different concentrations of MWCNTs under both PEG-induced stress and non-stress growing conditions were consequence of changes in the activation of various cellular antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (POD). Taken together, our findings reveal that MWCNTs played negative role on seed germination and subsequent growth of C. pepo L. seedlings under both levels of water potential.