In plants, hydrogen gas (H2) enhances tolerance to several abiotic stresses, including salinity and heavy metals. However, the effect of H2 on fungal growth under different stresses remains largely unclear. In this study, hydrogen-rich water (HRW) was employed to characterize physiological roles and molecular mechanisms of H2 in the alleviation of three different stresses in basidiomycete Hypsizygus marmoreus. Our results showed that HRW treatment, of which the H2 concentration was 0.8 mM, significantly reduced the toxicities of CdCl2, NaCl and H2O2, leading to significantly improved mycelial growth and biomass. These beneficial effects could be attributed to a significantly decreased formation of malondialdehyde (MDA). Besides, HRW treatment significantly increased the activities of antioxidants (SOD, CAT and GR) as well as the gene expressions of these antioxidants (SOD, CAT, and GR) at the mRNA level. In vivo detection of reactive oxygen species (ROS), including H2O2 and O2
−, as well as lipid peroxidation provided further evidence that HRW could significantly improve tolerances of CdCl2, NaCl and H2O2. Furthermore, pyruvate kinase was activated in the mycelia treated with HRW, along with its induced gene expression, suggesting that HRW treatment enhanced the glucose metabolism. Taken together, our findings suggested that the usage of HRW could be an effective approach for contaminant detoxification in H. marmoreus, which was similar with the effects of HRW in plants, and such effects could be also beneficial in entire agricultural system.Electronic supplementary materialThe online version of this article (doi:10.1186/s13568-017-0406-1) contains supplementary material, which is available to authorized users.