Seawater factory farming is an important fisheries industry in China and a modern, high-density, intensive farming model that is receiving increasing attention as it develops. Factory farming uses circulating water culture, in which water treatment technology is key. Timely removal of waste (bait, feces) from aquaculture tanks is an important means to improve water quality. In this study, the characteristics of the flow field and waste distribution in the pool were studied in a square circle cutaway model tank (mainly used for shrimp aquaculture), in which water flow was driven by a side-tube hydraulic jet to optimally conserve water and provide a reference for engineering factory farming pools. The flow field distribution is the main factor that directly affects the waste concentration in a recirculating aquaculture tank. We investigated the effects of jet flow velocity and angle on the flow field distribution and waste concentration characteristics in the tank. The flow field characteristics were measured with a point-type flow meter and were analyzed using MATLAB software. The waste distribution characteristics were obtained using self-developed image analyzing software. The original waste distribution images were captured with a high resolution camera. The results showed that flow velocity varied in a V type trend along the sections and through the center of the tank. Waste gathered more rapidly and at a higher concentration as jet velocity was increased at a fixed jet flow angle. The optimal jet angle was 40° when jet flow velocity was fixed at 24 cm/s. These results will be useful to optimize and design a hydraulic drive system for industrial fish or shrimp aquaculture tanks. The results suggest a jet angle of 40° with as high as possible jet flow velocity to ensure optimal animal growth.