Continually increasing demands on aquaculture products drive the current monoculture to upgrade and upscale because of not only economic but environmental sustainability reasons. Over the past decade, open water integrated multi-trophic aquaculture (IMTA) practiced as a potential alternative has been demonstratively illustrated from both scientific and public attention. Basing on previous studies of this synergistic aquaculture system, we, here, studied the physical environment in Onagawa Bay as the cornerstone for further IMTA implementation. Onagawa Bay locates in Miyagi Prefecture, Japan, and because of its mature practice on polyculture, it is recognized as a suitable site for IMTA. Unfortunately, the earthquake and tsunami in 2011 caused a huge uncertainty on physical environment changes. Still insufficient researches have been conducted on physical environment study, especially through modelling method. Here, adopting the three-dimensional Marine Environmental Committee (MEC) ocean model, we described the setup and validation for Onagawa Bay in this research. At the present stage, simulation results can best fit observation data on the tidal elevation with the correlation coefficient between observed and simulated tidal elevation reaching 0.96, captured the main characteristic of flow velocity, and exhibited homogenous tendency towards water temperature. Furthermore, through the plot of the residual velocity field and statistical seasonal velocity distribution, potential aquaculture configuration has been discussed spatio-temporally on the hypothesis that high current speeds contribute to the further implementation.