BACKGROUND The potential effect of chromium on the denitrification process has drawn much attention recently. The efficient remediation of groundwater contaminated by both hexavalent chromate [Cr(VI)] and nitrate (NO3-) was hampered due to the deficiency of denitrification in the presence of Cr(VI). The goal of this work was to understand the mechanisms of how Cr(VI) affected denitrification. RESULTS To better understand the underlying nature, Cr(VI) effects on denitrification were investigated in batch. Negative effects of Cr(VI) exposure on denitrification were confirmed and ascribed to restriction of bacterial activities, by regulating functional genes expression and altering community composition. Stronger inhibition of the expression of denitrifying genes was observed with increased Cr(VI) loading (0-50 mg L-1). The critical inhibitory concentration and IC50 of Cr(VI) on electron transport system activities were calculated to be 3.21 and 4.87 mg L-1, respectively. Further amplicon analysis revealed that Betaproteobacteria were enriched, implying their potential key role in simultaneously removing nitrate and Cr(VI). The presence of Cr(VI) also upregulated the metabolic activities related to apoptosis. CONCLUSION These findings shed light on the biogeochemical fates of Cr(VI) and NO3- in aquifers, and may contribute in enhancing their practical application for bioremediation using microbial processes. (c) 2019 Society of Chemical Industry