Aquaculture workers manually count the number of fish at regular intervals from hatching until they are shipped. To address this laborious task, this paper proposes a system for counting farmed juveniles utilizing a standard video camera. In the proposed system, a slide is installed, and a video camera is mounted above it to capture the surface. As juvenile fish flow down the slide along with water, the video is recorded and processed to count the number of fish captured. A tracking start and end lines are prepared within the video frame, and when a fish region crosses the start line, the count is incremented and the tracking starts. Then, all regions that have started tracking are subsequently tracked, and if occlusion by multiple fish is resolved during tracking, the count is incremented again. Experiments were conducted on 500 juvenile fish of each of three species, and the results showed that the counting accuracy exceeded 90% for all species, confirming the effectiveness of the proposed method.