The barrier layer, the layer between the bottom of the density-defined mixed layer and the isothermal layer in the upper ocean, may play a role in air-sea dynamics. In the present study, data from Argo profiling floats in the tropical Indian Ocean and a mooring at 90°E, 0°N are used to examine subseasonal variations in upper ocean salinity and barrier-layer thickness (BLT) during boreal winter. In the eastern equatorial Indian Ocean, subseasonal variations in BLT are energetic. However, composites used to isolate the Madden-Julian Oscillation (MJO) component of the subseasonal signal reveal that, on average, the MJO anomaly in BLT is negligible despite large swings in both the mixed-layer depth and the isothermal-layer depth. This discrepancy is likely due to (a) noise from other subseasonal processes; and (b) the diversity of individual MJO events: the thickness of the mixed layer and the isothermal layer are sensitive to wind and rain forcing, so even subtle differences in the phasing and strength of MJO-related atmospheric anomalies can produce a very different effect on upper ocean stratification and hence on the thickness of the barrier layer. The effect of the barrier layer on the upper ocean response to MJO forcing is also evaluated. When the barrier layer is thick, entrainment cooling during the MJO is reduced, so the MJO drives a weaker sea surface temperature anomaly. This suggests that modulation of BLT can have significant consequences for the response of the upper ocean to the MJO, and hence, potentially, for feedbacks of the ocean onto the atmosphere on MJO time scales. Key Points MJO excites systematic anomalies in MLD but not BLT Zonal advection dominates MJO salinity anomalies at 90°E, 0°N When the barrier layer is thin, the MJO excites stronger SST anomalies © 2014. American Geophysical Union. All Rights Reserved.