A compact helicopter-based lidar system is developed and tested under laboratory and field conditions. It is shown that the lidar can measure concentrations of chlorophyll a and dissolved organic matter at the surface of water bodies, detect fluorescence spectra of ground vegetation at a distance of up to 530 m, and determine the vertical profile of light-scattering particle concentration in the upper ocean. The possibilities of the lidar system are demonstrated by detection of polluted areas at the ocean surface, by online monitoring of three-dimensional distribution of light-scattering layers, and by recognition of plant types and physiological states.