Objectives Microbial agents with good effects of deodorization were screened to reduce the problem of environmental pollution caused by foul odors in manure water from aquaculture. Methods Samples were taken from river sediment sewage and livestock manure sewage. The plate streaking separation method was used to isolate bacterial strains from samples selected. The removal rate of NH₃ and H₂S by the bacterial strains was detected with the boric acid absorption method and the zinc amine complex salt absorption method. The strains with good effects of deodorization were screened to construct a combination of microbial agents for deodorization experiments in manure water from aquaculture. Results 18 bacterial strains were isolated from 2 samples, with 4 strains had good effect of reducing NH₃ and 1 strain had good ability to reduce NH₃ and H₂S. The screened 5 strains of bacteria B5, B6, B7, B8, and B9 were identified as Bacillus subtilis, Alcaligenes faecalis, Klebsiella pneumoniae, Bacillus licheniformis, and Bacillus cereus, respectively. The best removal rate of NH₃ and H₂S by the combination of microbial agent C (B5∶B9∶B8=1∶1∶1) in manure water from aquaculture was 87.39% and 59.57%, respectively. Conclusions The combination of microbial agent C has a good effect of deodorization in manure water from aquaculture, which can provide reference for the industrial production of microbial agents with highly efficient deodorization.