This project is a complex dataset associated with 16S amplicon sequencing data and metagenomic data from sediment samples from different locations and different depths in a coastal sea area, the Bohai Sea. Three sediment cores were sampled from the station BHB10, M3, and M8. Each sediment cores were sub-sampled at 2 cm intervals. Each sub-sample was sequenced with specific primers targetting bacterial and archaeal communities, respectively. Fifteen of the sub-samples from the sediment cores plus another 19 surface sediment samples from different locations were sequenced for metagenomes