Marine biologists traditionally determine the presence and quantities of different types of fish by dragging nets across the bottom, and examining their contents. This method, although accurate, kills the collected fish, damages their habitat, and consumes large quantities of resources. This paper presents an alternative, a machine vision system capable of determining the presence of fish species. Illumination presents a unique problem in this environment, and the design of an effective illumination system is discussed. The related issues of object orientation and measurement are also discussed and resolved. Capturing images of fish in murky water also presents challenges. An adaptive thresholding technique is required to appropriately segment the fish from the background in these images. Mode detection, and histogram analysis are useful tools in determining these localized thresholds. It is anticipated that this system, created in conjunction with the Rutgers Institute for Marine and Coastal Science, will effectively classify fish in the estuarine environment.