Airborne bathymetric lidar has proven to be a valuable sensor for rapid and accurate sounding of shallow water areas. With advanced processing of the lidar data, detailed mapping of the sea floor with various objects and vegetation is possible. This mapping capability has a wide range of applications including detection of mine-like objects, mapping marine natural resources, and fish spawning areas, as well as supporting the fulfillment of national and international environmental monitoring directives. Although data sets collected by subsea systems give a high degree of credibility they can benefit from a combination with lidar for surveying and monitoring larger areas. With lidar-based sea floor maps containing information of substrate and attached vegetation, the field investigations become more efficient. Field data collection can be directed into selected areas and even focused to identification of specific targets detected in the lidar map. The purpose of this work is to describe the performance for detection and classification of sea floor objects and vegetation, for the lidar seeing through the water column. With both experimental and simulated data we examine the lidar signal characteristics depending on bottom depth, substrate type, and vegetation. The experimental evaluation is based on lidar data from field documented sites, where field data were taken from underwater video recordings. To be able to accurately extract the information from the received lidar signal, it is necessary to account for the air-water interface and the water medium. The information content is hidden in the lidar depth data, also referred to as point data, and also in the shape of the received lidar waveform. The returned lidar signal is affected by environmental factors such as bottom depth and water turbidity, as well as lidar system factors such as laser beam footprint size and sounding density.