Exposure to inorganic arsenic (iAs) through drinking water is a major public health concern affecting most countries. Epidemiologic studies showed a significant association between consumption of iAs through drinking water and different types of cancer. However, the exact mechanisms underlying As-induced cancer and other diseases are not yet well understood. The aim of this study is to determine the effects of exposure iAs (20 or 30 mg/L) on Vicia faba seedlings in terms of phytotoxicity, genotoxicity, and spectroscopy by investigation of molecular modifications using infrared (FTIR) and near infrared (FTNIR) spectroscopy. Further, the mitigation effects of a precursor of glutathione (GSH), N-acetylcysteine (NAC), were also assessed. Spectroscopic and genotoxicity analysis demonstrated that specific molecular changes were directly correlated with iAs exposure. Comet assay in Vicia faba showed significant effects at concentrations of 20 and 30 mg/L, depending on the structural changes involving nucleic acids as identified by FTIR and FTNIR spectroscopy. Results of phytotoxicity and micronuclei tests were significant only at higher iAs concentrations (30 mg/L), where an antioxidant effect of NAC was noted. The two spectroscopic techniques demonstrated molecular modifications predominantly associated with chemical interactions of iAs with biomolecules such as nucleic acids, carbohydrates, lipids, and proteins in Vicia faba. Our findings suggest that further studies are required to better understand the mechanisms underlying toxicity produced by different As chemical forms in vegetal and agricultural species.