The accumulation of nitrate in recirculating aquaculture system constrains the sustainable development of aquaculture industry. This study evaluated the performance of two heterotrophic sulfur autotrophic denitrification (HSAD) reactors packed with PBAT/starch granules and supplemented with thiosulfate in the influent, operating at salinities of 0 ‰ (Reactor I) and 25 ‰ (Reactor II) over a 163-day period. Reactor I achieved an average nitrate removal rate of 0.17 kg/m3/d with minimal accumulation of nitrite, total ammonia nitrogen (TAN) and dissolved organic carbon (DOC). In contrast, Reactor II exhibited a slower start-up, a lower denitrification rate of 0.08 kg/m3/d, and higher fluctuations in water quality parameters. Over time, both reactors transitioned from heterotrophic to sulfur autotrophic denitrification, as evidenced by increased effluent sulfate concentration, acidification and a decline in microbial biomass. Metagenomics and metatranscriptomics analyses revealed the coexistence of autotropic and heterotrophic denitrifying bacteria, with salinity inhibiting the abundance of denitrifying bacteria and expression of functional genes associated with nitrogen and sulfur metabolism. Network analysis further identified positive correlations among microorganisms involved in carbon, nitrogen and sulfur cycling. This study provides insights into the microbial mechanisms in HSAD process and offers a promising approach for the treatment of nitrate-rich aquaculture wastewater.