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In this study, a sulfur-based autotrophic denitrifying filter (SADF) was developed for the purpose of removing nitrate from simulated recirculating mariculture wastewater. Results showed that over 90% of the nitrate could be effectively eliminated by utilizing thiosulfate as the electron donor, with a molar ratio of thiosulfate-S to nitrate molar ratio of 2:1 or greater. Additional batch tests confirmed that thiosulfate was a suitable sulfur source for nitrate removal even without prior accumulation of the biomass to nitrite. Excess thiosulfate had a minor impact on N-removal efficiency, so an external sulfur source was not required for nitrate removal, however, it could still help to reduce nitrate accumulation and water replacement to some extent. High-throughput sequencing results illustrated that <i>Thiomicrospira</i> and <i>Thioalkalivibrio</i> were the dominant autotrophic denitrifying genera in the SADF, while <i>Thiomicrospira</i> was more significantly affected in the case of insufficient sulfur sources. As the issue of nitrate accumulation in the mariculture recirculating system has been resolved, only a small amount of water needs to be added to the system daily. Therefore, the thiosulfate-based SADF process has the potential to be implemented for nitrate removal in mariculture systems, which could present a promising sustainable solution to the nitrate pollution issue.