Hydrogenotrophic denitrifiers are important bacteria for nitrate removal in wastewater and aquifers. Here, we report the complete genome sequences of three hydrogenotrophic denitrifiers, namely, Dechloromonas denitrificans strain D110, Ferribacterium limneticum strain F76, and Hydrogenophaga taeniospiralis strain H3, all of which were isolated from a nitrate-polluted aquifer in Bavaria (Germany).