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The basin-scale wave propagation in the Southern Indian Ocean (SIO) is inferred to affect the low-frequency variability of eddy kinetic energy (EKE) within the Agulhas current system (ACS). Observations and numerical simulations indicate that westward-propagating waves, in the form of sea level variability from the east boundary, may cause "non-linear" oceanic responses (e.g., sea level and EKE) in the ACS. This is likely due to two factors: (i) the movement of wave crests and troughs continuously alters the stratification of the upper ocean, generating a positive baroclinic instability and prompting conversions of EKE from mean flow in the source regions, and (ii) wave-current interactions induce a rapid intension of an anticyclone gyre in the interior SIO and the corresponding EKE in the downstream regions. These basin-scale wave modulations may provide an additional perspective to the traditional wind driving view based on the barotropic Sverdrup relation. The local winds over the SIO play an important role in maintaining basin-scale Rossby waves in the southwest Indian Ocean and further modulating oceanic low-frequency variability in a "quasi-linear" way. • The basin-scale wave propagation in the Southern Indian Ocean (SIO) have an influence on the dynamics of the Agulhas current system. (ACS). • The waves can alter the stratification of the upper ocean, as well as strengthen the anticyclone gyre in the interior SIO and the corresponding EKE in the downstream regions. • These basin-scale wave modulations may provide an additional perspective to the traditional wind driving view based on the barotropic Sverdrup relation. [ABSTRACT FROM AUTHOR]