A two wavelength lidar imaging system for underwater applications is presented which employs image subtraction. More specifically, a two wavelength lidar system is presented wherein two substantially simultaneously timed laser pulses of different wavelengths are emitted and are expanded by optics to illuminate the water below. A framing camera is then gated to receive light reflected or scattered back from the water. The light backscattered is filtered through narrow pass filters before it is recorded at the gated cameras. A specific application is disclosed in which the lidar imaging system is used to detect the passage of internal waves or other anomalies appearing in the ocean.