Appropriately used, computational fluid dynamics models are powerful tools to design and optimize primary settling tanks (PSTs). This paper uses a Fluent-based 3D model to identify the possible causes for underperformance of the circular PSTs at the Cali waste-water treatment plant, Colombia, and to propose design modifications to improve performance. A new configuration for the center well (CW) is proposed and evaluated. The influence of a rotational sludge scraper and of continuous sludge removal were considered in the numerical simulation. The new configuration included the modification of the current CW diameter and the location of a second baffle with the CW. The results suggest that the installation of the second baffle allows a more uniform flow distribution within the PST and consequently, the hydrodynamic problems associated with short-circuiting of the influent to the bottom of the tank are reduced. The second baffle suppresses the downward current, effectively dissipates the kinetic energy in the influent and forces the particles to move toward the bottom of the PST. In addition, the second CW baffle allows the formation in the inlet zone of a consistently more concentrated sludge blanket layer and thicker sludge, reducing the risk of solids leaving in the effluent of the PST.