Abstract: Solid particles (such as residual feed and feces) can often be produced by fish in aquaculture tanks. These particles can be naturally accumulated to cause the water pollution, even damage to the fish quality. The accumulation of such particles can also induce the adverse conditions for fish health and growth in aquaculture systems. It is very critical issue on the waste and contaminants for the sustainable environment. In this study, a six-degree-of-freedom (6-DOF) motion platform was utilized to simulate the rolling motion of aquaculture vessels. The self-cleaning performance of aquaculture tanks was examined under different rolling excitations. Two key parameters were characterized by: rolling amplitude (Θ) and rolling period (T), as well as the acute angle (α) between the water inlet pipe jet direction and the adjacent inclined wall. The self-cleaning process was divided into two interconnected components: the accumulation characteristics of contaminants and the flow field distribution inside the tank. Two elements were closely related with the flow field driven by the driving force for the accumulation of contaminants, while the efficiency of accumulation, in turn, dominated the flow field dynamics. The dynamic feedback loop among these components was ultimately represented the overall self-cleaning performance of the tank. Therefore, the tank designs and operational strategies were optimized to minimize the contamination for the high-quality of aquaculture environments. Several key findings revealed that the accumulation time was jointly regulated by both the rolling amplitude and the rolling period, indicating a complex variation under different conditions. The accumulation time initially increased but then decreased, as the rolling amplitude and period increased. Specifically, the minimal impact on the self-cleaning performance was achieved, when the rolling period and amplitude were set to 8 s and 1°, respectively. The particles accumulation was nearly identical to the static case. Once the rolling period was reduced to 4 s and the amplitude increased to 2°, there was the significant improvement in the self-cleaning performance. Among them, the accumulation time was reduced by approximately 70.6%, compared with the minimal condition. Both the period and amplitude of rolling motion were optimized to enhance the self-cleaning efficiency of the tank. Furthermore, there was the important influence of the water inlet pipe jet angle (α) on the accumulation. The accumulation time first increased then decreased, as the jet angle increased. Consequently, there were the shortest accumulation time and the best self-cleaning performance at a jet angle of α = 45°. This angle was corresponded to the most efficient distribution of flow within the tank, leading to the optimal transport of contaminants toward the designated outflow areas. The jet angle was then optimized to maximize the self-cleaning efficiency. In terms of flow field, there was the substantial impact of the variation in the rolling period and amplitude on the internal flow dynamics of the aquaculture tank. The deceasing rolling period and increasing rolling amplitude were resulted in an expansion of high-flow regions and the central vortex within the tank, which in turn led to a higher average water velocity. This increasing flow rate was also reduced the accumulation time and rate. Additionally, the flow field was found to be most uniform at α = 45° under various jet angles, which was aligned with the strongest accumulation among all tested jet angles. Therefore, the self-cleaning performance of the aquaculture tank was achieved in the short rolling period and high rolling amplitude. At the same time, the excessively high velocities of water was potentially resulted in the operational challenges, such as energy consumption and instability in the tank environment. Therefore, the appropriate sea areas can be expected to ensure the optimal performance in practical applications, in order to balance the rolling motion and then fine-tune the water inlet pipe jet angle. As such, the quality of aquaculture products can be maintained to optimize the operational efficiency. Overall, this finding can provide the valuable theoretical support and scientific evidence to optimize the self-cleaning performance of aquaculture vessels under rolling excitations. A better understanding was also gained on the dynamics of contaminant accumulation and flow field distribution in the aquaculture systems. Some important implications can also be obtained to improve the sustainable operations in the deep-sea aquaculture. More efficient and environmentally friendly aquaculture practices can greatly contribute to the aquaculture industry with less environmental impact.