This dataset includes regional subsets in the western Indonesian region of output from a run of the Parallel Ocean Program (POP) version 2, the ocean component of the Community Earth System Model (CESM). The model was run with nominal 0.1-degree horizontal resolution, and 62 vertical levels with 10 meter resolution above 160 meters and gradually increasing vertical spacing below this level. The run was forced with Coordinated Ocean-Ice Reference Experiments (CORE) Version 2 atmospheric reanalyses, derived from NCEP reanalysis and remote sensing products. The model integration was coupled to the Los Alamos Sea Ice Model (CICE) version 4 using Coupler 7 (CPL7) in the CESM framework. The data files encompass the geographic range 85-130 E longitude, 15S-5N latitude, with all depth levels included. 5-day averages of state variables, surface fluxes, and advective fluxes of temperature and salinity are archived for the years 1977-2009 (the first two years are considered a transition period from climatological forcing). The high resolution and multidecadal time span of the output make it ideal for studying mesoscale eddies, coastal waves, and topography-constrained ocean flows and their long-term variability.