2018 Elsevier Ltd Propagation of a lidar beam in a coupled atmosphere-ocean model consisting of multiple atmospheric and upper oceanic layers and a rough ocean surface is studied by using a vectorized Monte Carlo radiative transfer solver optimized specifically for lidar-based remote sensing applications. The effects of assumed phytoplankton morphology variations and its vertical distribution on the lidar attenuated backscatter and depolarization ratio are studied. In this study, a phytoplankton particle is assumed to be a sphere, a sphere with a core, or a randomly distorted hexahedron with or without a core. The single-scattering properties of the nonspherical/inhomogeneous particles are computed using appropriate state-of-the-art light-scattering computational capabilities. Vertical variation of the phytoplankton distribution is derived explicitly using a PAR (photosynthetically active radiation) limited carbon biomass balance equation that is subsequently coupled with the Monte Carlo solver.