The lockdown measures that were taken to combat the COVID-19 pandemic minimized anthropogenic activities and created natural laboratory conditions for studying air quality. Both observations and WRF-Chem simulations show a 20-50% reduction (compared to pre-lockdown and same period of previous year) in the concentrations of most aerosols and trace gases over Northwest India, the Indo Gangetic Plain (IGP), and the Northeast Indian regions. It is shown that this was mainly due to a 70-80% increase in the height of the boundary layer and the low emissions during lockdown. However, a 60-70% increase in the pollutants levels was observed over Central and South India including the Arabian sea and Bay of Bengal during this period, which is attributed to natural processes. Elevated (dust) aerosol layers are transported from the Middle East and Africa via long-range transport, and a decrease in the wind speed (20-40%) caused these aerosols to stagnate, enhancing the aerosol levels over Central and Southern India. A 40-60% increase in relative humidity further amplified aerosol concentrations. The results of this study suggest that besides emissions, natural processes including background meteorology and dynamics, play a crucial role in the pollution concentrations over the Indian sub-continent.