An eddy-resolving Indo-Pacific ocean circulation model was applied to highlight the behavior of eddies throughout the Indonesian seas. The complexity of the topography and coastline at the entrance of the Makassar Strait induce an eddy-type throughflow, instead of a straightforward flow. A sill and a narrow passage in the Makassar strait creates a barrier and impedes the continuation of eddies from the Pacific ocean, but the existence of a steep deep basin (>500 m depth) between the Java and Flores seas indicates a possible area for eddies. Based on our numerical results, we described the presence of a unique eddy structure north of Lombok Island, which we designated the “Lombok Eddy” and verified it by performing a drifter release field experiment and reviewing monthly mean climatology data from the World Ocean Atlas 2001 and XBT PX2 track data. NCEP/NCAR reanalysis, satellite observation data, and mixed layer depth analysis were also used to confirm these processes. By analyzing numerical simulation results and available temperature datasets, two additional eddies were found. All eddies form primarily due to eastward local winds correlated with seasonal monsoon winds during the austral summer. These eddies vary synchronously at an interannual time scale. Together, they are referred to as the Lombok Eddy Train (LET), which affects the surface layer down to a depth of 60 m, and the intensity of the eddy system is strongly affected by mixed layer depth variability from December to February.