Abstract Saline wastewater is a big challenge for the application of anammox processes. Although the feasibility of freshwater anammox bacteria for saline wastewater treatment was revealed, its metabolic acclimation to different saline concentrations is still elusive. Here, one low-strength-fed anammox reactor was operated with the shift of saline concentrations. The results showed that one Ca. Brocadia genome with a relative abundance of 31.5% was recovered. Meta-Omics analyses showed that salinity (around 12.5 g L −1 NaCl) could promote the nitrogen transformation in Ca. Brocadia through the driven of dissimilatory nitrate reduction to ammonium (DNRA). Specific sodium translocations pump (Na + -NADH:quinone oxidoreductase), as well as more genes associated with H + - dependent membrane-bound ATP formation and Na + -dependent membrane-bound ATP formation, was highly expressed in Ca. Brocadia under saline conditions than that under fresh conditions. This implied that such Na + transduction was likely associated with the NADPH/NADH via the hydrazine oxidation pathway. Notably, sodium extrusion was also associated with energy exploitation from the hydrolysis of pyrophosphatase (PPi) through K + -stimulated pyrophosphate-energized sodium pump. This study shed light on the metabolic acclimation, such as nitrogen transformation and cation-induced energy transduction (i.e., Na + , K + , and Ca 2+ ) in Ca. Brocadia, illustrating their feasibility for saline and freshwater wastewater treatment. • Ca. Brocadia AMX1 with low similar (<81.8%) to published strains was enriched. • Salinity of 12.5 g L −1 NaCl promoted nitrogen transformation in Ca. Brocadia AMX1 . • The cation-induced energy transductions are verified in Ca. Brocadia AMX1 . • The hydrolysis of pyrophosphatase (PPi) can provide energy for sodium extrusion. • Metabolic linkage of nitrogen conversion and cations transductions were discussed.