Long-term measurements of the extinction index of water were carried out with a shipboard lidar in the North Atlantic Ocean. Sensing was performed through the rough air-water interface. Three-week sensing at one geographical site has demonstrated that in case of changing water masses of different origin the dependence of the extinction index on the temperature of water has the form of a linear regression due to the activity of phytoplankton. Lidar measurements are compared with independent measurements of the depth of visibility of a standard white disc (Secchi disc). Some peculiarities of lidar return signals are discussed in case of shipboard lidar sensing of water. A method has been suggested to compensate for the effect of foam and surf caused by sailing ship on the accuracy of the lidar measurements.