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The Regional Indian Ocean model based on Modular Ocean Model (MOM4p1) was used to understand the importance of a realistic representation of bathymetry on Ocean General Circulation. The model has 1/4° uniform horizontal resolution and is forced with Coordinated Ocean-Ice Reference Experiments (CORE-II) inter-annual forcing with two simulations named BLND (realistic bathymetry) and OM3 (smoothed bathymetry), which only differ in the representation of bathymetry for the years 1992-2005. We also used recent reanalysis products from ORAS5 and SODA3 and ADCP observation to compare the subsurface currents. We show that by the inclusion of realistic bathymetry, there is a significant improvement in the upper ocean salinity, temperature, and currents, particularly near the coast. The salinity and temperature of the upper ocean are very close to the observed value near the coast. The bias in the salinity and temperature was reduced to half in BLND simulation compared to OM3, which led to a more realistic East India Coastal Current (EICC). We show the first evidence of a basin-wide cyclonic gyre over the Bay of Bengal at 1000 m depth during spring, which is just opposite to that of a basin-wide anti-cyclonic gyre at the surface. We found the presence of poleward EICC during spring at 1000 m and 2000 m depth, which is opposite to that of the surface. The presence of this deeper EICC structure is completely absent during fall. We show the presence of a boundary current along the coast of Andaman and Nicobar Island at a depth of 2000 m. The observed Wyrtki Jet (WJ) magnitude and spatial structure are most realistically reproduced in BLND simulation as compared to OM3 simulations. Both ORAS5 and SODA reanalysis products underestimate the WJ magnitude. The presence of the Maldives Islands is responsible for the westward extent of Equatorial Under Current (EUC). The presence of Maldives also creates wakes on the leeward side in the EUC zonal current. During fall, EUC is better defined in the eastern Equatorial Indian Ocean and lies at a depth of between 50 and 100 m, unlike its spring counterpart, in which its core is located slightly deeper, between 100 and 150 m depth. During peak summer months, June-July, a strong eastward zonal jet is present at 1000 m depth, similar to Wyrtki Jet (WJ). Inter-monsoon Jets, i.e., spring and fall jets, are also seen but are in the opposite direction, i.e., westward, unlike eastward in WJ.