Switchgrass (Panicum virgatum L.) is a warm perennial grass with valuable characteristics as a biofuel crop. To avoid competition with food crops, biofuel crops will be likely relegated to less productive soils such as marginal lands. Consequently, the salinity and water scarcity problems that commonly affect marginal lands compromise biofuel crop germination, emergence, and seedling establishment. The aims of this study were to study the germination and seedling growth of switchgrass under salinity and water stress and to describe the morpho-anatomical responses of the roots and leaves in the seedlings to these stress conditions. The effect of salt and water stress was assessed using sodium chloride (NaCl) and polyethylene glycol (PEG) 8000 at the same water potentials of − 0.8, − 1.0, and − 1.2 MPa. Seeds were moist prechilled for 7 days at 5 °C and germinated at 30/15 °C (8 h light/16 h dark). NaCl treatments (− 0.8 and − 1.0 MPa) delayed germination rates but did not reduce the final germination percentage, whereas at a lower potential (− 1.2 MPa), the final germination percentage was diminished. The effects of PEG (− 1.0 and − 1.2 MPa) on the germination rate and final percentage were more detrimental than those induced by isosmotic concentrations of NaCl. PEG and NaCl reduced significantly the vigor index of − 0.8 to − 1.2 MPa. The morphoanatomical changes such as the reduction in the root cross-sectional area and the thickening of the endodermis walls for both stress conditions and aerenchyma formation in the cortex under salinity could significantly contribute in the survival and tolerance during the early seedling stages.