To protect the lacquer plates from the Nanhai No. 1 shipwreck from being corroded by microorganisms, a series of studies were conducted on the four water-stored samples. The water samples were collected from the vessel where the lacquerware was stored in June and December 2017. In our study, high-throughput sequencing was conducted to reveal predominant bacterial communities. Then, three different media were used to isolate the dominant bacteria, and the 16S rRNA genes were sequenced. Next, we tested the degradation activity of lignin and cellulose by the isolated bacterial strains. After being cultured on a medium containing carboxylmethylcellulose (CMC), almost all the isolated strains (except Microbacterium sp. NK-NH4, Ochrobactrum sp. NK-NH9, and Bacillus megaterium NK-NH10) showed the capacity for cellulose degradation. In addition, the lignin peroxidase (Lip) and laccase activity of the strains were shown by culturing the strains on one medium with azure and on another medium with Remazol brilliant blue. The results indicated that the Lip activity of all the strains was low, whereas the laccase activity of Microbacterium sp. NK-NH4, Bacillus tequilensis NK-NH5, Bacillus subtilis NK-NH6, Bacillus megaterium NK-NH10, and Bacillus velezensis NK-NH11 was relatively high. Finally, we tested the bacteriostatic efficacy of four biocides—Preventol® D7, BIT 20N, P91, and Euxyl® K100. We found that most strains were sensitive to D7 and 20N, while K100 had almost no impact.