Abstract Accurately representing small‐scale bathymetry in ocean modeling is challenging, as it requires high‐resolution bathymetry observations and high‐resolution model grids. However, it is crucial for the representation of global ocean circulation. The Indonesian Seas, key region for global atmospheric and oceanic circulations, feature a complex topography of deep and shallow seas, islands, and straits. Our study investigates the importance of horizontal resolution and bathymetry on the Indonesian Throughflow by comparing simulations at different resolutions (1/10° $1/10{}^{\circ}$, 1/25° $1/25{}^{\circ}$, and 1/100° $1/100{}^{\circ}$) and two 1/25° $1/25{}^{\circ}$ simulations with varied bathymetry. Results show that higher resolution and smoother bathymetry modify the regional circulation and its associated transport by up to 30% and locally by up to 80%. Temperature distribution displays differences of up to 2° ${}^{\circ}$C between resolutions, highlighting the influence of small‐scale processes and bathymetry on ocean dynamics. Our results can provide a guide for tuning or parameterizing processes for coarser simulations of the Indonesian Seas.

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