Counting and tracking fish populations is important for conservation purposes as well as for the fishing industry. Various non-invasive automatic fish counters exist based on such principles as resistivity, light beams and sonar. However, such methods typically cannot make distinction between fish and other passing objects, and moreover, cannot recognize different species. Computer vision techniques provide an attractive alternative for building a more robust and versatile fish counting systems. In this paper we present the fish detection framework for noisy videos captured in water with low visibility. For this purpose, we compare three background subtraction methods for the task. Moreover, we propose necessary post-processing steps and heuristics to detect the fish and separate them from other moving objects. The results showed that by choosing an appropriate background subtraction method, it is possible to achieve a satisfying detection accuracy of 80% and 60% for two challenging datasets. The proposed method will form a basis for the future development of fish species identification methods.