The H(2)-based membrane biofilm reactor (MBfR) was used to remove nitrate and perchlorate from real ion-exchange brine at two different salinities (30- and 50-g/L NaCl). Base production from nitrate reduction to N(2) gas caused the pH to increase, and this exacerbated precipitation of calcium and magnesium carbonates onto the MBfR fibers. The precipitates lowered the H(2) flux to the biofilm and caused a deterioration of denitrification performance that could be reversed by mild citric-acid washing. The addition of acid seems to be the only mechanism to avoid serious precipitation, membrane fouling, and non-optimal pH for denitrification.