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Global and local stresses such as increased water temperature and terrestrial sediment runoff significantly affect coral reef ecosystems. Over the past three decades, the increase in the intensity and frequency of coral bleaching has been a significant problem in tropical and subtropical coastal seas, and maintaining healthy coral reef ecosystems has long been a challenge. Coral cover in Shimajiri Bay on Kume Island, located in the Nansei Islands (Okinawa Prefecture, southern Japan), has declined due to exposure to high water temperatures, an outbreak of coral predators, and sediment (red soil) inflow from the land. From such a background, coral aquaculture has been implemented at a few stations in the bay. Therefore, it is essential to conduct aquaculture in suitable locations for coral growth and survival. This study aimed to select suitable locations for coral culture with high spatial resolution in an enclosed bay that was greatly affected by red soil runoff, mainly from a sugarcane field. A freshwater and red soil runoff model for the watershed was merged with a coastal hydrodynamic, red soil dispersal, and accumulation model at a spatial resolution of 75 m for Shimajiri Bay. The simulation results were validated using in situ continuous and routine observations. Simulations were conducted over ten years. Locations not subjected to high water temperature in the bay or river loading were selected based on topography, simulated water temperature, salinity, and red soil content of sea sediment. This coupled model enables us to evaluate the growth and survival conditions of cultured corals with high spatiotemporal resolution and quantitatively consider the reduction target of red soil runoff to realize robust coral growth and survival. • We coupled sediment runoff model, hydrodynamic model and sediment dispersal model. • We simulated spatio-temporal variations in water temperature and terrestrial load. • We estimated priority sites for coral aquaculture in a small bay in southern Japan. [ABSTRACT FROM AUTHOR]