Groundwater co-contaminated by vanadium (V) (V(V)) and nitrate requires efficient remediation to prevent adverse environmental impacts. However, little is known about simultaneous bio-reductions of V(V) and nitrate supported by gaseous electron donors in aquifers. This study is among the first to examine microbial V(V) reduction and denitrification with hydrogen as the sole electron donor. V(V) removal efficiency of 91.0 ± 3.2% was achieved in test bioreactors within 7 d, with synchronous, complete removal of nitrate. V(V) was reduced to V(IV), which precipitated naturally under near-neutral conditions, and nitrate tended to be converted to nitrogen, both of which processes helped to purify the groundwater. Volatile fatty acids (VFAs) were produced from hydrogen oxidation. High-throughput 16S rRNA gene sequencing and metagenomic analyses revealed the evolutionary behavior of microbial communities and functional genes. The genera Dechloromonas and Hydrogenophaga promoted bio-reductions of V(V) and nitrate directly coupled to hydrogen oxidation. Enriched Geobacter and denitrifiers also indicated synergistic mechanism, with VFAs acting as organic carbon sources for heterotrophically functional bacteria while reducing V(V) and nitrate. These findings are likely to be useful in revealing biogeochemical fates of V(V) and nitrate in aquifer and developing technology for removing them simultaneously from groundwater.