Wireless optical communication (WOC) through the atmosphere–ocean system is fundamentally complex because of the diversity, concentration, types and vertical thickness of the constituents and poses a major challenge from the optical characteristics of bubbles at the air–sea interface and water constituents (phytoplankton, suspended sediments, and dissolved organic matter), and stratification (medium inhomogeneity). The present study aims to analyse the effects of atmospheric aerosols (their intensity, diversity, and vertical thickness), waves/bubbles at the air–sea interface, seawater constituents (phytoplankton, suspended sediments, and dissolved organic matter), and medium inhomogeneity along the path between a laser transmitter in the airborne platform and a receiver in the underwater platform using Monte Carlo technique. For the first time, our analysis showed that for a homogeneous atmosphere–ocean channel (7 km in the atmosphere column and 42 m in the ocean medium), the estimated normalized received power reduced to 17 dB and the time delay spread increased to 1.01 ns (considering a receiver of 7” and an aperture FOV of 180°) when compared to those values for a stratified atmosphere–ocean channel. The bubbles (both clean and coated) relative to the particulates in open oceanic water under high wind speeds have a significant impact on the spatio-temporal spread of the laser beam. There is also a well pronounced effect of coated bubbles on the received signal power in open ocean water. In contrast, the particulates have a higher impact on the received signal power than the clean/coated bubbles in turbid coastal water. These results suggest that the normalized received power when calculated for the cases of dense bubble populations under high wind speeds (at a wind speed 18 ms−1) reduced to 8–9 dB and increased to 0.0025 scintillation index. The coated bubbles at the air–water interface reduced the normalized received power by 1.41 dB compared to the clean bubbles. Further, our analysis indicated that the expansion of beam width and the reduction of beam divergence angle can be utilized to mitigate the performance degradation (power loss) caused by bubbles at the air–sea interface. These results and analyses will be helpful for a system designer to accurately define/decide the system parameters and build a functional communication system for the inhomogeneous atmosphere–ocean system.