Barley (Hordeum vulgare L.) is a crucial cereal crop globally, and its productivity is influenced by environmental factors, including elevated carbon dioxide (CO2) levels and water stress. The aim of this study is to investigate the effects of water stress and increased CO2 concentration on the growth, physiological responses, and yield of two-row and six-row barley genotypes. Univariate data analysis revealed significant effects of CO2 concentration on most traits except chlorophyll a (Chla), crop antioxidant capacity as evaluated by the activity of plant extracts to scavenge the 2,2-diphenyl-1-picrylhydrazyl (DPPH), and on the maximum quantum yield of photosystem II (Fv/Fm). Mean comparisons showed that elevated CO2 increased certain traits such as shoot dry weight (ShDW) (34.1%), root dry weight (RDW) (50.8%), leaf area (LA) (12.5%), grain weight (GW) (64.1%), and yield-related traits and combination of significant indices (CSI) (72.5%). In comparison, Proline (−19.3%), Malondialdehyde (MDA) (−34.4%) levels, and antioxidant enzyme activities, including ascorbate peroxidase (APX) (−39.1%), peroxidase (POX) (−26.1%), and catalase (CAT), (−34.4%) decreased. Water stress negatively affected ShDW (−40.2%), GW (−43.7%), RDW (−28.5%), and LA (−28.8%), while it positively affected DPPH (36.0%), APX (54.8%), CAT (85.1%), and MDA (101%). Six-row barley genotypes (Goharan and Mehr) had the highest yield under normal humidity and elevated CO2 concentrations, while under water stress conditions, their yield decreased more than two-row genotypes (Behrokh and M9316). Principal component analysis and heatmapping revealed that two-row barley genotypes exhibited the highest stress resistance under elevated CO2 concentrations, with the highest levels of secondary metabolites.