Abstract Previous studies have hypothesized that climatologically thick salinity-stratified barrier layers (BLs) in the north Indian Ocean (NIO) influence the upper ocean heat budget, sea surface temperature (SST), and monsoons. Here, we investigate how state-of-the-art Coupled Model Intercomparison Project phase 6 (CMIP6) climate models simulate the NIO barrier layer thickness (BLT). CMIP6 models generally reproduce the BLT seasonal cycle and spatial distribution, but with shallow November–February (NDJF) biases in regions with thick observed BLT: the eastern equatorial Indian Ocean (EEIO), Bay of Bengal (BoB), and southeastern Arabian Sea (SEAS). We show that the intensity of the CMIP6 equatorial easterly wind bias controls the EEIO shallow isothermal layer depth (ILD) and BLT biases. It also controls the BoB shallow BLT bias, both through the propagation of the EEIO shallow ILD bias into the NIO coastal waveguide and because it is linked to the BoB dry and cold bias through the Bjerknes feedback, hence also controlling the mixed layer depth (MLD) deep bias there. Finally, the SEAS shallow BLT bias is due to a too-deep MLD, in response to subdued monsoonal currents around India, which do not bring enough BoB low-salinity water. The BL insulating effect mentioned in literature does not seem to dominate in CMIP6. Rather, the CMIP6 salinity-related deep MLD biases diminish the BoB cooling rate by winter upward surface heat fluxes, reducing cold SST biases. This suggests that salinity effects alleviate the easterly equatorial wind, cold, and dry BoB biases that develop through the positive Bjerknes feedback loop in CMIP6.