Atmospheric aerosols over the oceanic region are very important air pollutant and play a vital role in Earth’s radiation budget and climate change. This study presents the aerosol climatology over the Bay of Bengal (BoB) and Arabian sea (AS) using long term (2006–2012) data from space-borne radiometers [Moderate-Resolution Imaging Spectroradiometer (MODIS), Ozone Monitoring Instrument (OMI)] and space-based active lidar onboard Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO). AS experiences higher AOD as compared to that over BoB during the study period. A good periodicity along with strong intra-seasonal/annual variability in aerosol loading is also observed over both the study regions. Approximately one month lag is found for maximum aerosol loading period over AS and BoB for almost every year i.e., June–July for AS and May–June for BoB. This lag could be explained by pathway and timing of summer monsoon over the Indian subcontinent. Elevated layers of absorbing dust up to 2–4 km altitudes are observed during the pre-monsoon and monsoon seasons over both the regions. The CALIPSO measurements show strong seasonal heterogeneity in aerosol properties over both the regions, which is well corroborated with MODIS and OMI observations. This significant seasonal heterogeneity in aerosol loading has been explained by the role of transportation of aerosols from various emission sources using NOAA HYSPLIT back trajectory model at three different altitude levels viz. 500, 1500 and 2500 m height. The possible role of Indian summer monsoon in modulating the aerosol behaviour over AS and BoB is another important aspect of this study that need further analyses using higher spatio-temporal resolution data.