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In this work, in-situ remediation of sediment was carried out by combining various methods. The results showed that the treatment effect of Calcium nitrate + composite functional microorganisms + Low-DO (dissolved oxygen) aeration (CN/CFM/LDA) was the best, in which 2.5 g calcium nitrate, 1 g functional bacteria and intermittent aeration (0.1 m3/h, 3 h per day) were utilized for the remediation of 500 g sediments within 40-day experimental period. The DO and oxidation reduction potential (ORP) in overlying water have been improved from 3.23 mg/L to 4.4 mg/L and 25.8 mV to 112.4 mV, respectively. The release fluxes of ammonia nitrogen (NH 4 +-N), nitrite nitrogen (NO 2 −-N) and nitrate nitrogen (NO 3 −-N) were respectively reduced by 30.51%, 13.11% and 77.45% compared with the control and the removal rate of the acid volatile sulfide (AVS) in sediments was 94.14% compared with the original sample. The results of high-throughput sequencing show that the dominant bacterial community in CN/CFM/LDA was transformed into Proteobacteria (relative abundance of 74.17%) at the phylum level and Thiobacillus (relative abundance of 38.52%) at the genus level. The results of 16S functional prediction indicated that the remediation method can enhance the numbers of microbial key enzymes (92360) in the nitrification and denitrification process, where Low-DO aeration can mediate the growth of denitrifying bacteria and promote the performance of key enzymes. In conclusion, the experimental results show that the use of calcium nitrate and composite functional microorganisms under low-DO regulation has a promising remediation effect on sediments of black-malodorous water. Unlabelled Image • A novel method of combination of repair agents and Low-DO aeration to mitigate the release of nitrogen into water. • The color of the sediments also changed from black to yellowish brown. • The dominant bacterial community in sediments transformed into Proteobacteria at the phylum level. • Low-DO aeration can mediate the growth of denitrifying bacteria and promote the performance of key enzymes. [ABSTRACT FROM AUTHOR]