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Nitric oxide (NO) and hydrogen sulphide (H 2 S) are important gaseous signalling molecules that regulate key physiochemical mechanisms of plants under environmental stresses. A number of attempts have been made to improve waterlogging tolerance in plants, but with limited success. Having said that, NO and H 2 S are vital signalling molecules, but their role in mitigating waterlogging effects on crop plants is not well established.• We investigated the efficacy of exogenous NO and H 2 S to alleviate waterlogging effects in two wheat cultivars (Galaxy-2013 and FSD-2008).• Waterlogging produced a noticeable reduction in plant growth, yield, chlorophyll, soluble sugars and free amino acids. Besides, waterlogging induced severe oxidative damage seen as higher cellular TBARS and H 2 O 2 content. Antioxidant enzyme activity increased together with a notable rise in Fe 2+ and Mn 2+ content. Proline content was higher in waterlogged plants compared with non-waterlogged plants. In contrast, waterlogging caused a substantial decline in endogenous levels of essential nutrients (K + , Ca 2+ and Mg 2+ ). Waterlogged conditions led to Fe 2+ and Mn 2+ toxicity due to rapid reduction of Fe 3+ and Mn 3+ in the soil.• Exogenous NO and H 2 S significantly protected plants from waterlogging effects by enhancing the oxidative defence and regulating nutritional status. Besides, the protective effects of exogenous NO were more prominent as compared with effects of H 2 S. Further, we did not study the effect of H 2 S and NO on photosynthetic attributes and expression of stress-related genes. Therefore, future studies should examine the effects of H 2 S and NO on wheat physiology and gene expression under waterlogging.