Selenate (SeO42-) reduction in hydrogen (H-2)-fed membrane biofilm reactors (H-2-MBfRs) was studied in combinations with other common electron acceptors. We employed H-2-MBfRs with two distinctly different conditions: R1, with ample electron-donor availability and acceptors SeO42- and sulfate (SO42-), and R2, with electron-donor limitation and the presence of electron acceptors SeO42-, nitrate (NO3-), and SO42-. Even though H-2 was available to reduce all input SeO42- and SO42- in R1, SeO42- reduction was preferred over SO42- reduction. In R2, co-reduction of NO3- and SeO42- occurred, and SO42- reduction was mostly suppressed. Biofilms in all MBfRs had high microbial diversity that was influenced by the "rare biosphere" (RB), phylotypes with relative abundance less than 1%. While all MBfR biofilms had abundant members, such as Dechloromonas and Methyloversatilis, the bacterial communities were significantly different between R1 and R2. For R1, abundant genera were Methyloversatilis, Melioribacter, and Propionivibrio; for R2, abundant genera were Dechloromonas, Hydrogenophaga, Cystobacter, Methyloversatilis, and Thauera. Although changes in electron-acceptor or -donor loading altered the phylogenetic structure of the microbial communities, the biofilm communities were resilient in terms of SeO42- and NO3- reductions, because interacting members of the RB had the capacity of respiring these electron acceptors.