Using two membrane biofilm reactors in which hydrogen (H2) was the only exogenous electron donor, we studied the microbial community structure of biofilms composed primarily of denitrifying bacteria (DB) and sulfate-reducing bacteria (SRB). In steady-state EDvSS, H2 availability was restricted and varied. In steady-state EAvSS, the input nitrate () concentration was varied relative to a fixed sulfate () concentration. SRB co-existed with DB, even when reduction was absent due to restricted H2 availability. UniFrac and principal coordinate analysis indicated that H2 availability and electron-acceptor loadings framed the microbial community structure, with H2 availability having a greater impact. In EDvSS, restricted H2 availability favored heterotrophic DB (i.e. Burkholderiales) compared with autotrophic DB (e.g. Hydrogenophilales and Rhodocyclales). In EAvSS, reduction lowered the relative abundance of some DB (e.g. Hydrogenophilales), and the biofilm was colonized by Desulfovibrionales and Bacteroidales. Reinforcing the impact of H2 availability, EAvSS showed a higher microbial diversity and more even distribution among microbial groups than did EDvSS. Thus, the biofilm community in a H2-fed biofilm with DB and SRB became more heterotrophic when the H2 availability was constrained, while low loading allowed more reduction, causing a shift to more SRB.