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This study investigated the effect of salinity on microbial composition and denitrification capacity of woodchip bioreactors treating recirculating aquaculture system (RAS) effluents. Twelve laboratory-scale woodchip bioreactors were run in triplicates at 0, 15, 25, and 35 ppt salinities, and water chemistry was monitored every third day during the first 39 days of operation. Microbial communities of the woodchips bioreactors were analyzed at the start, after one week, and at the end of the trial. Woodchip bioreactors removed nitrate at all salinities tested. The highest NO3-N removal rate of 22.0 ± 6.9 g NO3-N/m3/d was obtained at 0 ppt, while 15.3 ± 4.9, 12.5 ± 5.4 and 11.8 ± 4.0 g NO3-N/m3/d were obtained at salinities of 15, 25 and 35 ppt, respectively. Nitrate removal rates thus decreased with salinity, being 54–69% lower than at 0 ppt. Leaching of total ammonia nitrogen (TAN) and orthophosphate (PO4-P) from woodchips was initially higher at saline treatments compared to 0 ppt, while initial leaching of BOD5 appeared to be similar across all treatments. Production of alkalinity per g NO3-N removed was higher at 0 (3.6 ± 0.5 gCaCO3/gNO3-N) and 15 ppt (3.5 ± 0.8) than at the more saline treatments (25 ppt: 2.0 ± 0.9, 35 ppt: 1.12 ± 0.5 gCaCO3/gNO3-N), indicating that heterotrophic denitrification was the dominant nitrate removing process at 0 and 15 ppt, while autotrophic denitrification processes probably interfered with the alkalinity balance at 25 and 35 ppt. In the woodchip reactors, Gammaproteobacteria was the most abundant taxa. However, salinity shaped the woodchip microbiome, resulting in an increase in the abundance of sulfide oxidizing autotrophic denitrifiers, but decrease in the overall abundance of denitrifying microbes at higher salinities, which presumably explained the reduced nitrate removal rates at elevated salinities. This study demonstrates that woodchip bioreactors can be applied to remove nitrate from saline RAS effluents albeit at lower nitrate removal rates compared to freshwater installations.