In this paper, we present the experimental data of seawater sensing using an airborne lidar with a changeable field of view, as well as the results of numerical simulations of the lidar operation by the Monte Carlo method. It is shown that the influence of sea waves leads to the increase of the rate of the return signal fall off with the increasing depth and to overestimation of the extinction coefficient measured at small field-of-view angles of the lidar receiver. Another cause of inefficient sensing with small field-of-view angles is strong fluctuations of the lidar return power, which cannot be described by normal distribution. At large field-of-view angles, multiple scattering partly compensates for the effect of sea waves. Applicability of simple models of the sea surface to description of the fluctuations of lidar return power is discussed.