Stratification of the upper few meters of the ocean limits the penetration depth of wind mixing and the vertical distribution of atmospheric fluxes. Significant density stratification at depths ≤ 5 m was observed in 38% of a 2‐month data set from the central Indian Ocean collected during the DYNAMO experiment (Dynamics of the MJO, Madden‐Julian Oscillation). Diurnal warm layers (DWLs) formed by solar heating populated 30% of the data set and rain layers (RLs) populated 16%. Combined contributions from rain and insolation formed RL‐DWLs in 9% of the data set. RLs were detected at values of U10 up to 9.8 m s−1, while DWLs were only detected at U10 < 7.6 m s−1 (99th percentile values), symptomatic of the greater buoyancy flux provided by moderate to high rain rate compared to insolation. From the ocean friction velocity, u*w, and surface buoyancy flux, B, we derived estimates of
htruêS, stable layer depth, and
UtruêS, the maximum U10 for which stratification should persist at
htruêS for fixed B. These estimates predicted (1) 36 out of 44 observed stratification events (88% success rate) and (2) the wind limits of these events, which are considered to be the 99th percentile values of U10). This suggests a means to determine the presence of ocean stable layers at depths ≤ 5 m from U10 and B. Near‐surface stratification varied throughout two Madden‐Julian Oscillation (MJO) cycles. In suppressed MJO periods, (U10 ≤ 8 m s−1 with strong insolation), RLs and RL‐DWLs were rare while DWLs occurred daily. During disturbed and active MJO periods, (U10 ≤ 8 m s−1 with increased rain and cloudiness), multiple RLs and RL‐DWLs formed per day and DWLs became less common. When westerly wind bursts occurred, (U10 = 7–17 m s−1 with steady rain), RLs formed infrequently and DWLs were not detected.