A computerized system of performing fish census which otherwise requires high level of domain knowledge and expertise is described. Divers with minimal knowledge of fish can obtain high quality population and species distribution measurements using a stereo camera rig and fish video analyzer software that was developed. The system has two major components: a camera rig and software for fish size, density and biomass estimation. The camera rig consists of a simple stand on which one to four pairs of stereo cameras are mounted to take videos of the benthic floor for a few minutes. The collected videos are uploaded to a server which performs stereo analysis and image recognition. The software produces video clips containing estimates of fish size, density and species biodiversity and a log report containing information about the individual fishes for further end user analysis.