Developing impressive and cost-effective desalination technologies is crucial for addressing the increasing global demand for freshwater. In this regard, along with the process type and technology of desalination, the system's efficiency relies on the availability of a sufficient, constant, uniform, and high-quality discharge flow from the seawater intake structure. This investigation concerns the discharge flow performance of velocity caps, which serve as submerged seawater intake structures, in unsteady flows using physical models and decision tree algorithms. The observations indicate that the square caps are more prone to instability compared to the circular caps when exposed to waves. Additionally, circular caps can increase efficiency by about 12 % compared to square caps. Therefore, the circular velocity cap is more optimal than the square one. Results show that increasing wave height and period decreases the discharge through the intake due to increased interaction between wave and intake structure. Also, wave steepness leaves a significant reverse effect on seawater intake of about 40 %. The study also found that the optimal relative bottom height (w/h) is 1 for high flow depths and 0.5 for low flow depths, respectively. Finally, practical equations of discharge coefficients have been proposed based on decision tree algorithms with high accuracy. These high-accuracy equations show great potential for designing new desalination systems and optimizing existing ones.