In recirculating aquaculture systems (RASs), ammonia excreted by fish must be converted to the less toxic nitrate before recirculation. Nitrifying microorganisms in biofilters used for this transformation can be sensitive to changes in salinity, which can present issues for systems that raise anadromous fish such as Atlantic salmon. Freshwater biofilters maintained at a low level of salinity (such as biofilters operated in coastal areas) may be better equipped to handle more drastic salinity shifts; therefore, experiments were performed on freshwater and low-salinity (3 ppt) biofilters to assess their ability to recover nitrification activity after an abrupt change in salinity (3, 20, and 33 ppt). Two-week tests showed full nitrification recovery in freshwater biofilters after a shift to 3 ppt but no ammonia oxidation in 20 or 33 ppt. Low-salinity-adapted filters (transitioned from 0 to 3 ppt) showed a small recovery (about 11%) after a shift to 20 ppt, and no activity when shifted to 33 ppt. Illumina sequencing revealed that, while nitrification was slowed or stopped with shifting salinities, the nitrifiers survived the salinity increases; conversely, the heterotrophic communities were more greatly affected and were reduced in proportion with increasing salinity. This work indicates that biofilters operated at low salinity may recover more quickly after large salinity changes, though this slight benefit may not outweigh the cost of low-level salinity maintenance. Further research into halotolerant heterotrophs in biofilms may increase the effectiveness of nitrifying biofilters under variable salinities.