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 (NO₃⁻) concentration was varied relative to a fixed sulfate (SO₄²⁻) concentration. SRB co-existed with DB, even when SO₄²⁻ 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, SO₄²⁻ 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 NO₃⁻ loading allowed more SO₄²⁻ reduction, causing a shift to more SRB.