The increasing coastal urbanization and need for resilience against natural disasters have driven the development of floating structures, such as a three-layer floating ground system proposed by Shimizu Corporation. However, a persistent challenge for virtually all floating structures in water has been biofouling, posing uncertainty for floating project succeed. To evaluate potential impacts on aquatic environment, a pilot study utilizing floating substrata was conducted in Tokyo Bay from August 2022 to March 2023. Monitoring of water quality revealed seasonal variations in the aquatic habitat. Typically, hypoxic conditions and low salinity concentrations characterized the water during the summer and fall seasons, whereas the winter seasons witnessed a decline in water temperatures and chlorophyll a concentration. However, monitoring of sessile organism attachment elucidated a generally linear increase in organism growth. Moreover, the relationship between habitat characteristics and sessile organism biomass was assessed and compared to data from the 2000s. Surprisingly, the dominant species of this investigation, comprising nearly 95% of the total individuals and wet biomass, was the small brown mussel (Xenostrobus securis). However, two decades ago, the Tokyo Bay shoreline was inhabited predominantly by the blue mussel (Mytilus galloprovincialis). Deviations in this relationship are now attributed to biotic factors, such as parasite outbreaks, and abiotic factors, including climate change and anthropogenic impacts. Notably, this pilot experiment has triggered an ongoing, comprehensive investigation in Tokyo Bay.