In order to elucidate microbial response to the benthic environment in trench and flat seabed sediments, dynamic changes in the sediment microbial community and the water quality of overlying water were evaluated during summer and autumn in Tokyo Bay, Japan. A large amount of nutrients accumulated in the trench during summer when stratification occurred, which stimulated the sediment microbial growth, resulting in higher microbial density compared to the flat seabed sediment. Additionally, predominant ubiquinone species in the two sediments were ubiquinone with 9 isoprene units (Q-9) and Q-8, respectively, while menaquinone with 6 isoprene units (MK-6) dominated. Hence, the different bottom shapes were expected to produce distinct microbial environments. In autumn, the convective mixing of seawater resulted in the disappearance of stratification and the deposition of nutrients onto the flat seabed sediment, which contributed to excessive microbial growth. During this transition period, Q-containing bacteria dominated with lag time instead of MK-containing bacteria. At the same time, the molar fraction of MK-6 that might correspond to sulfate-reducing bacteria also rapidly decreased. However, this microbial change was not observed in the trench since it kept anaerobic conditions longer. Multidimensional scaling analysis indicated that dissolved oxygen of the bottom water can drive microbial community shift.