This study is based on the analysis of the measurement of ozone and water vapor by airbus in-service aircraft (MOZAIC) data of vertical ozone (O3) and carbon monoxide (CO) over Hyderabad during November 2005–March 2009. Measurements in the upper troposphere show highest values of O3 (53–75 ppbv) and CO (80–110 ppbv) during the pre-monsoon and post-monsoon seasons, respectively. The episodes of strong wind shears (>20 ms−1) were frequent during the monsoon/post-monsoon months, while weak shear conditions (<10 ms−1) were prevalent during the winter season. The profiles of both O3 and CO measured under southerly winds showed lower values than under northerly winds in each season. The strong and weak wind shears over the study region were associated with the El Niño and La Niña conditions, respectively. The outgoing long-wave radiation (OLR) and wind shear data indicate enhancement in the convective activity from monsoon to post-monsoon period. Higher levels of O3 were measured under the strong shear conditions, while CO and H2O show enhancements under weak shear conditions. The near surface observation and simulations show increase of O3 with increasing OLR, while insignificant relation in the upper region. In case of CO, the MOZAIC and CCM2 show weaker dependence while MOZART-4 shows rapid increase with OLR indicating large overestimation of convective transport. A modified Tiedtke convective scheme provides better representation compared to the Hack/Zhang-McFarlane schemes for both O3 and CO during the monsoon season. The difference between observation and simulations were particularly large during transition from El Niño to La Niña phases. The different convection scheme and horizontal resolution in the MOZART-4 and CCM2 seem to be the major causes of disagreement between these models. Vertical profiles of both O3 and CO during extreme events such a tropical cyclones (TCs) show strong influence of the convective-dynamics over Bay of Bengal (BOB). © 2016, Springer-Verlag Berlin Heidelberg.