The effects of aeration and stirring systems on the physical properties of sludge were analyzed using a computational fluid dynamics (CFD) model. The aims of this study were to (1) compare the effects of aeration and stirring on sludge properties using the same turbulent mixing intensity, and (2) to reveal the relationship between sludge properties and hydrodynamic indicators to determine how hydrodynamic conditions influence sludge flocculation. Mixing experiments with stirring and aeration were carried out in 2-L beakers with the average velocity gradient (G) set to 90, 190, or 280 s. The sludge flocculation performance, zeta potential, and Gibbs free energy (ΔG) were analyzed and the flow velocity, turbulence energy, turbulence dissipation rate, and Kolmogorov microscale were calculated as hydrodynamic parameters. The average flow velocity and the turbulence dissipation rate were obviously higher in the stirring system than in the aeration system at the same G. However, the turbulence energy and Kolmogorov microscale in the aeration system were much higher than those in the stirring system. Both the zeta potential and ΔG were lower in the aeration system than the stirring system. The zeta potential and ΔG results for the two systems suggest that aeration is more beneficial for sludge flocculation than stirring even though the sludge flocculation performance F/F in the stirring and aeration systems showed no obvious differences. Significant relationships between hydrodynamic parameters calculated based on the CFD model and average values of sludge properties in the stable phase showed that the Kolmogorov microscale, average flow velocity, and turbulence energy were appropriate hydrodynamic parameters for evaluating the flocculation performance F/F, zeta potential, and ΔG, respectively.